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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Duman, R."

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Search Summary

This query matches 62 Structures.

Refinements

Structure Determination Methodology

experimental (62)

Scientific Name of Source Organism

	Homo sapiens (20)
	Escherichia coli (6)
	Cyanothece sp. PCC 7425 (5)
	Klebsiella pneumoniae (5)
	Lama glama (3)
	Bos taurus (2)
	Operophtera brumata cypovirus 18 (2)
	Pseudomonas sp. KKS102 (2)
	Pseudorabies virus Ea (2)
	Thaumatococcus daniellii (2)

More...

Taxonomy

	Eukaryota (28)
	Bacteria (27)
	Riboviria (4)
	Archaea (2)
	Duplodnaviria (2)
	other sequences (1)
	unclassified sequences (1)

Experimental Method

	X-RAY DIFFRACTION (61)
	ELECTRON MICROSCOPY (1)

Polymer Entity Type

	Protein (59)
	DNA (4)
	RNA (1)

Refinement Resolution (Å)

	1.0 - 1.5 (2)
	1.5 - 2.0 (17)
	2.0 - 2.5 (18)
	2.5 - 3.0 (17)
	3.0 - 3.5 (5)
	3.5 - 4.0 (3)

Release Date

	2010 - 2014 (3)
	2015 - 2019 (16)
	2020 - 2024 (43)

Enzyme Classification Name

	Isomerases (2)
	Hydrolases (2)
	Lyases (2)
	Transferases (2)
	Oxidoreductases (1)
	Translocases (1)

Membrane Protein Annotation

	PDBTM (12)
	mpstruc (12)
	MemProtMD (9)
	OPM (2)

Symmetry Type

	Cyclic (34)
	Asymmetric (22)
	Dihedral (2)
	Icosahedral (1)

SCOP Classification

	Artifacts (3)
	All beta proteins (5)
	Alpha and beta proteins (a+b) (2)

AllSelected

1 to 25 of 62 Structures

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3ZIE \| pdb_00003zie	Download File View File

SepF-like protein from Archaeoglobus fulgidus

Duman, R., Ishikawa, S., Celik, I., Ogasawara, N., Lowe, J., Hamoen, L.W.

(2013) Proc Natl Acad Sci U S A 110: E4601

Released	2013-11-20
Method	X-RAY DIFFRACTION 2 Å
Organisms	Archaeoglobus fulgidus
Macromolecule	SEPF-LIKE PROTEIN (protein)

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3ZIG \| pdb_00003zig	Download File View File

SepF-like protein from Pyrococcus furiosus

Duman, R., Ishikawa, S., Celik, I., Ogasawara, N., Lowe, J., Hamoen, L.W.

(2013) Proc Natl Acad Sci U S A 110: E4601

Released	2013-11-27
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Pyrococcus furiosus COM1
Macromolecule	SEPF-LIKE PROTEIN (protein)

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3ZII \| pdb_00003zii	Download File View File

Bacillus subtilis SepF G109K, C-terminal domain

Duman, R., Ishikawa, S., Celik, I., Ogasawara, N., Lowe, J., Hamoen, L.W.

(2013) Proc Natl Acad Sci U S A 110: E4601

Released	2013-11-27
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Bacillus subtilis
Macromolecule	CELL DIVISION PROTEIN SEPF (protein)

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4X35 \| pdb_00004x35	Download File View File

A micro-patterned silicon chip as sample holder for macromolecular crystallography experiments with minimal background scattering

Roedig, P., Vartiainen, I., Duman, R., Panneerselvam, S., Stuebe, N., Lorbeer, O., Warmer, M., Sutton, G., Stuart, D.I., Weckert, E., David, C., Wagner, A., Meents, A.

(2015) Sci Rep 5: 10451-10451

Released	2015-06-10
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Operophtera brumata cypovirus 18
Macromolecule	Polyhedrin (protein)
Unique Ligands	ATP, CL, GTP, MG

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4X3B \| pdb_00004x3b	Download File View File

A micro-patterned silicon chip as sample holder for macromolecular crystallography experiments with minimal background scattering

Roedig, P., Vartiainen, I., Duman, R., Panneerselvam, S., Stuebe, N., Lorbeer, O., Warmer, M., Sutton, G., Stuart, D.I., Weckert, E., David, C., Wagner, A., Meents, A.

(2015) Sci Rep 5: 10451-10451

Released	2015-06-10
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Gallus gallus
Macromolecule	Lysozyme C (protein)
Unique Ligands	CL, NA

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4ZG3 \| pdb_00004zg3	Download File View File

In-vacuum long-wavelength crystallography

Wagner, A., Duman, R., Henderson, K., Mykhaylyk, V.

(2016) Acta Crystallogr D Struct Biol 72: 430-439

Released	2016-03-09
Method	X-RAY DIFFRACTION 1.2 Å
Organisms	Thaumatococcus daniellii
Macromolecule	Thaumatin-1 (protein)
Unique Ligands	GOL, NA, TLA

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5FB6 \| pdb_00005fb6	Download File View File

Room-temperature macromolecular crystallography using a micro-patterned silicon chip with minimal background scattering

Roedig, P., Duman, R., Sanchez-Weatherby, J., Vartiainen, I., Burkhardt, A., Warmer, M., David, C., Wagner, A., Meents, A.

(2016) J Appl Crystallogr 49: 968-975

Released	2016-06-15
Method	X-RAY DIFFRACTION 1.901 Å
Organisms	Sus scrofa
Macromolecule	Insulin Chain A (protein) Insulin Chain B (protein)

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5MQW \| pdb_00005mqw	Download File View File

High-speed fixed-target serial virus crystallography

Roedig, P., Ginn, H.M., Pakendorf, T., Sutton, G., Harlos, K., Walter, T.S., Meyer, J., Fischer, P., Duman, R., Vartiainen, I., Reime, B., Warmer, M., Brewster, A.S., Young, I.D., Michels-Clark, T., Sauter, N.K., Sikorsky, M., Nelson, S., Damiani, D.S., Alonso-Mori, R., Ren, J., Fry, E.E., David, C., Stuart, D.I., Wagner, A., Meents, A.

(2017) Nat Methods 14: 805-810

Released	2017-06-21
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Operophtera brumata cypovirus 18
Macromolecule	Polyhedrin (protein)
Unique Ligands	ATP, CL, GTP, MG

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5OSN \| pdb_00005osn	Download File View File

Crystal Structure of Bovine Enterovirus 2 determined with Serial Femtosecond X-ray Crystallography

Roedig, P., Ginn, H.M., Pakendorf, T., Sutton, G., Harlos, K., Walter, T.S., Meyer, J., Fischer, P., Duman, R., Vartiainen, I., Reime, B., Warmer, M., Brewster, A.S., Young, I.D., Michels-Clark, T., Sauter, N.K., Kotecha, A., Kelly, J., Rowlands, D.J., Sikorsky, M., Nelson, S., Damiani, D.S., Alonso-Mori, R., Ren, J., Fry, E.E., David, C., Stuart, D.I., Wagner, A., Meents, A.

(2017) Nat Methods 14: 805-810

Released	2017-08-30
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Enterovirus E
Macromolecule	Capsid protein (protein)
Unique Ligands	GLU, K, OSF, SO4, SPH

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5TCL \| pdb_00005tcl	Download File View File

Thaumatin from 4.96 A wavelength data collection

Aurelius, O., Duman, R., El Omari, K., Mykhaylyk, V., Wagner, A.

(2017) Nucl Instrum Methods Phys Res B 411: 12-16

Released	2017-09-20
Method	X-RAY DIFFRACTION 3.201 Å
Organisms	Thaumatococcus daniellii
Macromolecule	Thaumatin-1 (protein)
Unique Ligands	GOL, TLA

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6DZ1 \| pdb_00006dz1	Download File View File

Studies of Ion Transport in K+ Channels

Langan, P.S., Vandavasi, V.G., Weiss, K.L., Wagner, A., Duman, R., El Omari, K., Afonine, P.V., Coates, L.

(2018) Nat Commun 9: 4540-4540

Released	2018-11-14
Method	X-RAY DIFFRACTION 2.26 Å
Organisms	Bacillus cereus BDRD-Cer4
Macromolecule	Potassium channel protein (protein)
Unique Ligands	K, MPD

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6JJF \| pdb_00006jjf	Download File View File

Crystal structure of a two-quartet DNA mixed-parallel/antiparallel G-quadruplex

Zhang, Y.S., EI Omari, K., Duman, R., Wagner, A., Parkinson, G.N., Wei, D.G.

(2020) Nucleic Acids Res 48: 9886-9898

Released	2020-02-26
Method	X-RAY DIFFRACTION 1.47 Å
Organisms	Pseudorabies virus Ea
Macromolecule	DNA (5'-D(GPGPCPTPCPGPGPCPGPGPCPGPGPA)-3') (nucleic acid)
Unique Ligands	K, NA, NCO

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6JJH \| pdb_00006jjh	Download File View File

Crystal structure of a two-quartet RNA parallel G-quadruplex complexed with the porphyrin TMPyP4

Zhang, Y.S., EI Omari, K., Duman, R., Wagner, A., Parkinson, G.N., Wei, D.G.

(2020) Nucleic Acids Res 48: 9886-9898

Released	2020-02-26
Method	X-RAY DIFFRACTION 1.74 Å
Organisms	Pseudorabies virus Ea
Macromolecule	RNA (5'-R(GPGPCPUPCPGPGPCPGPGPCPGPGPA)-3') (nucleic acid)
Unique Ligands	K, POH

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6OWX \| pdb_00006owx	Download File View File

Spy H96L:Im7 L18pI-Phe complex; multiple anomalous datasets contained herein for element identification

Rocchio, S., Duman, R., El Omari, K., Mykhaylyk, V., Yan, Z., Wagner, A., Bardwell, J.C.A., Horowitz, S.

(2019) Acta Crystallogr D Struct Biol 75: 1084-1095

Released	2019-05-29
Method	X-RAY DIFFRACTION 2.06 Å
Organisms	Escherichia coli
Macromolecule	Periplasmic chaperone Spy (protein)
Unique Ligands	CL, IMD, IOD, ZN

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6OWY \| pdb_00006owy	Download File View File

Spy H96L:Im7 K20pI-Phe complex; multiple anomalous datasets contained herein for element identification

Rocchio, S., Duman, R., El Omari, K., Mykhaylyk, V., Yan, Z., Wagner, A., Bardwell, J.C.A., Horowitz, S.

(2019) Acta Crystallogr D Struct Biol 75: 1084-1095

Released	2019-05-29
Method	X-RAY DIFFRACTION 2.07 Å
Organisms	Escherichia coli
Macromolecule	Periplasmic chaperone Spy (protein)
Unique Ligands	CL, IMD, IOD, ZN

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6OWZ \| pdb_00006owz	Download File View File

Spy H96L:Im7 L19pI-Phe complex; multiple anomalous datasets contained herein for element identification

Rocchio, S., Duman, R., El Omari, K., Mykhaylyk, V., Yan, Z., Wagner, A., Bardwell, J.C.A., Horowitz, S.

(2019) Acta Crystallogr D Struct Biol 75: 1084-1095

Released	2019-05-29
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Escherichia coli
Macromolecule	Periplasmic chaperone Spy (protein)
Unique Ligands	CL, IMD, IOD, ZN

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6RTW \| pdb_00006rtw	Download File View File

Crystal structure of the Patched-1 (PTCH1) ectodomain in complex with nanobody NB64 and cholesterol-hemisuccinate

Rudolf, A.F., Kowatsch, C., El Omari, K., Malinauskas, T., Kinnebrew, M., Ansell, T.B., Bishop, B., Pardon, E., Schwab, R.A., Qian, M., Duman, R., Covey, D.F., Steyaert, J., Wagner, A., Sansom, M.S.P., Rohatgi, R., Siebold, C.

(2019) Nat Chem Biol 15: 975-982

Released	2019-10-02
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens Lama glama
Macromolecule	Llama-derived nanobody NB64 (protein) Protein patched homolog 1 (protein)
Unique Ligands	NAG, Y01

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6RTX \| pdb_00006rtx	Download File View File

Crystal structure of the Patched-1 (PTCH1) ectodomain 1

(2019) Nat Chem Biol 15: 975-982

Released	2019-10-02
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Homo sapiens
Macromolecule	Protein patched homolog 1 (protein)
Unique Ligands	NAG

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6RTY \| pdb_00006rty	Download File View File

Crystal structure of the Patched ectodomain in complex with nanobody NB64

(2019) Nat Chem Biol 15: 975-982

Released	2019-10-02
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens Lama glama
Macromolecule	Llama-derived nanobody NB64 (protein) Protein patched homolog 1 (protein)
Unique Ligands	NAG

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6RVC \| pdb_00006rvc	Download File View File

Crystal structure of Patched-1 ectodomain 2 (PTCH1-ECD2) in complex with nanobody 75

(2019) Nat Chem Biol 15: 975-982

Released	2019-10-02
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens Lama glama
Macromolecule	Nanobody NB75 (protein) Protein patched homolog 1 (protein)
Unique Ligands	NAG, SO4

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6RVD \| pdb_00006rvd	Download File View File

Revised cryo-EM structure of the human 2:1 Ptch1-Shh complex

El Omari, K., Rudolf, A.F., Kowatsch, C., Malinauskas, T., Kinnebrew, M., Ansell, T.B., Bishop, B., Pardon, E., Schwab, R.A., Qian, M., Duman, R., Covey, D.F., Steyaert, J., Wagner, A., Sansom, M.S.P., Rohatgi, R., Siebold, C.

(2019) Nat Chem Biol 15: 975-982

Released	2019-10-02
Method	ELECTRON MICROSCOPY 3.5 Å
Organisms	Homo sapiens
Macromolecule	Protein patched homolog 1 (protein) Sonic hedgehog protein (protein)
Unique Ligands	CA, CLR, NAG, PLM, ZN
Unique branched monosaccharides	NAG

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6TQI \| pdb_00006tqi	Download File View File

I-MOTIF STRUCTURE FORMED FROM THE C STRAND OF A HUMAN TELOMERE FRAGMENT

Parkinson, G.N., Wagner, A., Viladoms-Claverol, J., Duman, R., El-Omari, K.

(2020) Nucleic Acids Res 48: 9886-9898

Released	2020-06-10
Method	X-RAY DIFFRACTION 2.95 Å
Organisms	Homo sapiens
Macromolecule	DNA (5'-TPAPAPCPCPCPTPAP*A-3') (nucleic acid)

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6YO1 \| pdb_00006yo1	Download File View File

Crystal structure of ribonuclease A solved by vanadium SAD phasing

El Omari, K., Mohamad, N., Bountra, K., Duman, R., Romano, M., Schlegel, K., Kwong, H., Mykhaylyk, V., Olesen, C.E., Moller, J.V., Bublitz, M., Beis, K., Wagner, A.

(2020) IUCrJ 7: 1092-1101

Released	2020-11-04
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Bos taurus
Macromolecule	Ribonuclease pancreatic (protein)
Unique Ligands	UVC

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6YSO \| pdb_00006yso	Download File View File

Crystal structure of the (SR) Ca2+-ATPase solved by vanadium SAD phasing

El Omari, K., Mohamad, N., Bountra, K., Duman, R., Romano, M., Schlegel, K., Kwong, H., Mykhaylyk, V., Olesen, C.E., Moller, J.V., Bublitz, M., Beis, K., Wagner, A.

(2020) IUCrJ 7: 1092-1101

Released	2020-11-04
Method	X-RAY DIFFRACTION 3.13 Å
Organisms	Oryctolagus cuniculus
Macromolecule	Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 (protein)
Unique Ligands	128, CL, K, MG, TG1, VN4

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7O56 \| pdb_00007o56	Download File View File

X-ray Structure of Interferon Regulatory Factor 4 DNA binding domain bound to an interferon-stimulated response element solved by Phosphorus and Sulphur SAD methods

El Omari, K., Agnarelli, A., Duman, R., Wagner, A., Mancini, E.J.

(2021) Acta Crystallogr F Struct Biol Commun 77: 202-207

Released	2021-05-12
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Interferon regulatory factor 4 (protein) DNA (5'-D(PAPAPTPAPAPAPAPGPAPAPAPCPCPGPAPAPAPGPTPAPA)-3') (nucleic acid) DNA (5'-D(PTPTPTPAPCPTPTPTPCPGPGPTPTPTPCPTPTPTPTPAPT)-3') (nucleic acid)

1 to 25 of 62 Structures

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Membrane Protein Annotation

Symmetry Type

SCOP Classification

3ZIE | pdb_00003zie

3ZIG | pdb_00003zig

3ZII | pdb_00003zii

4X35 | pdb_00004x35

4X3B | pdb_00004x3b

4ZG3 | pdb_00004zg3

5FB6 | pdb_00005fb6

5MQW | pdb_00005mqw

5OSN | pdb_00005osn

5TCL | pdb_00005tcl

6DZ1 | pdb_00006dz1

6JJF | pdb_00006jjf

6JJH | pdb_00006jjh

6OWX | pdb_00006owx

6OWY | pdb_00006owy

6OWZ | pdb_00006owz

6RTW | pdb_00006rtw

6RTX | pdb_00006rtx

6RTY | pdb_00006rty

6RVC | pdb_00006rvc

6RVD | pdb_00006rvd

6TQI | pdb_00006tqi

6YO1 | pdb_00006yo1

6YSO | pdb_00006yso

7O56 | pdb_00007o56