RCSB PDB: Search

Warning You are using a web browser that we do not support. Our website will not work properly. Please update to a newer version or download a new web browser, such as Chrome or Firefox.

Help

Help

RCSB PDB

Deposit
- PDBx/mmCIF file
- pdb_extract
- SF-Tool
- Ligand Expo
- MAXIT
- Validation Server
- Validation API
- Information for Journals
- Validation Task Forces
- wwPDB OneDep System
- PDB-IHM
Search
Visualize
Analyze
Download
Learn
- Training Courses
- Guide to PDB Data
- Molecule of the Month
- Educational Resources
- Curricula
- Browse
- News
- SciArt Galleries
- Irving Geis
- David Goodsell
About
Careers
COVID-19

234,136 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

	Include CSM
Advanced Search \| Browse Annotations		Help

Search
Query History
Browse Annotations
MyPDB

QUERY: Gene Name = "dapA"

MyPDB Login

Search API

Advanced Search Query Builder

Help

Full Text

Structure Attributes

Help

NOT

Count

Add Subquery

Chemical Attributes

Sequence Similarity

Sequence Motif

Structure Similarity

Structure Motif

Chemical Similarity

Return

grouped by

Include Computed Structure Models (CSM)

Count

Clear

Search Summary

This query matches 37 Structures.

Refinements

Structure Determination Methodology

experimental (37)

Scientific Name of Source Organism

	Homo sapiens (32)
	Drosophila melanogaster (2)
	Mus musculus (2)
	Saccharomyces cerevisiae (1)
	synthetic construct (1)

Taxonomy

	Eukaryota (37)
	other sequences (1)

Experimental Method

	X-RAY DIFFRACTION (27)
	ELECTRON MICROSCOPY (5)
	SOLUTION NMR (5)

Polymer Entity Type

	Protein (37)
	DNA (2)

Refinement Resolution (Å)

	1.5 - 2.0 (1)
	2.0 - 2.5 (12)
	2.5 - 3.0 (7)
	3.0 - 3.5 (6)
	3.5 - 4.0 (1)
	4.0 - 4.5 (1)
	> 4.5 (4)

Release Date

	1990 - 1994 (1)
	1995 - 1999 (3)
	2000 - 2004 (2)
	2005 - 2009 (8)
	2010 - 2014 (9)
	2015 - 2019 (6)
	2020 - 2024 (8)

Enzyme Classification Name

	Hydrolases (9)
	Transferases (2)
	Ligases (2)

Membrane Protein Annotation

OPM (1)

Symmetry Type

	Asymmetric (22)
	Cyclic (10)
	Dihedral (5)

SCOP Classification

	All alpha proteins (12)
	Small proteins (4)
	Alpha and beta proteins (a+b) (2)
	Artifacts (3)
	All beta proteins (1)

AllSelected

1 to 25 of 37 Structures

Page 1 of 2

Sort by

Explore in 3D

1H9U \| pdb_00001h9u	Download File View File

The structure of the human retinoid-X-receptor beta ligand binding domain in complex with the specific synthetic agonist LG100268

Schwabe, J.W.R., Love, J.D., Gooch, J.T.

(2002) J Biological Chem 277: 11385

Released	2002-04-03
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Homo sapiens
Macromolecule	RETINOID X RECEPTOR, BETA (protein)
Unique Ligands	CL, LG2, NI

Explore in 3D

1HCP \| pdb_00001hcp	Download File View File

DNA RECOGNITION BY THE OESTROGEN RECEPTOR: FROM SOLUTION TO THE CRYSTAL

Schwabe, J.W.R., Rhodes, D., Neuhaus, D.

(1993) Structure 1: 187-204

Released	1995-11-23
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	HUMAN/CHICKEN ESTROGEN RECEPTOR (protein)
Unique Ligands	ZN

Explore in 3D

1HCQ \| pdb_00001hcq	Download File View File

THE CRYSTAL STRUCTURE OF THE ESTROGEN RECEPTOR DNA-BINDING DOMAIN BOUND TO DNA: HOW RECEPTORS DISCRIMINATE BETWEEN THEIR RESPONSE ELEMENTS

Schwabe, J.W.R., Chapman, L., Finch, J.T., Rhodes, D.

(1993) Cell 75: 567-578

Released	1995-11-23
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens
Macromolecule	PROTEIN (ESTROGEN RECEPTOR) (protein) DNA (5'-D(CPCPAPGPGPTPCPAPCPAPGPTPGPAPCPCPT PG)-3') (nucleic acid) DNA (5'-D(CPCPAPGPGPTPCPAPCPTPGPTPGPAPCPCPT PG)-3') (nucleic acid)
Unique Ligands	ZN

Explore in 3D

1HG4 \| pdb_00001hg4	Download File View File

Ultraspiracle ligand binding domain from Drosophila melanogaster

Schwabe, J.W.R., Clayton, G.M.

(2001) Proc Natl Acad Sci U S A 98: 1549

Released	2001-02-23
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Drosophila melanogaster
Macromolecule	ULTRASPIRACLE (protein)
Unique Ligands	LPP

Explore in 3D

1XC5 \| pdb_00001xc5	Download File View File

Solution Structure of the SMRT Deacetylase Activation Domain

Codina, A., Love, J.D., Li, Y., Lazar, M.A., Neuhaus, D., Schwabe, J.W.R.

(2005) Proc Natl Acad Sci U S A 102: 6009-6014

Released	2005-05-03
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Nuclear receptor corepressor 2 (protein)

Explore in 3D

1ZFD \| pdb_00001zfd	Download File View File

SWI5 ZINC FINGER DOMAIN 2, NMR, 45 STRUCTURES

Neuhaus, D., Nakaseko, Y., Schwabe, J.W.R., Rhodes, D., Klug, A.

(1992) J Mol Biology 228: 637-651

Released	1996-10-14
Method	SOLUTION NMR
Organisms	Saccharomyces cerevisiae
Macromolecule	SWI5 (protein)
Unique Ligands	ZN

Explore in 3D

2DRP \| pdb_00002drp	Download File View File

THE CRYSTAL STRUCTURE OF A TWO ZINC-FINGER PEPTIDE REVEALS AN EXTENSION TO THE RULES FOR ZINC-FINGER/DNA RECOGNITION

Fairall, L., Schwabe, J.W.R., Chapman, L., Finch, J.T., Rhodes, D.

(1993) Nature 366: 483-487

Released	1994-08-31
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Drosophila melanogaster
Macromolecule	PROTEIN (TRAMTRACK DNA-BINDING DOMAIN) (protein) DNA (5'-D(CPTPAPAPTPAPAPGPGPAPTPAPAPCPGPTPC PCPG)-3') (nucleic acid) DNA (5'-D(TPCPGPGPAPCPGPTPTPAPTPCPCPTPTPAPT PTPA)-3') (nucleic acid)
Unique Ligands	ZN

Explore in 3D

2L5G \| pdb_00002l5g	Download File View File

Co-ordinates and 1H, 13C and 15N chemical shift assignments for the complex of GPS2 53-90 and SMRT 167-207

Oberoi, J., Yang, J., Neuhaus, D., Schwabe, J.W.R.

(2011) Nat Struct Mol Biol 18: 177-184

Released	2011-02-02
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	G protein pathway suppressor 2 (protein) Putative uncharacterized protein NCOR2 (protein)

Explore in 3D

2MWI \| pdb_00002mwi	Download File View File

The structure of the carboxy-terminal domain of DNTTIP1

Schwabe, J.W.R., Muskett, F.W., Itoh, T.

(2015) Nucleic Acids Res 43: 2033-2044

Released	2015-02-18
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Deoxynucleotidyltransferase terminal-interacting protein 1 (protein)

Explore in 3D

2VSR \| pdb_00002vsr	Download File View File

hPPARgamma Ligand binding domain in complex with 9-(S)-HODE

Itoh, T., Fairall, L., Schwabe, J.W.R.

(2008) Nat Struct Mol Biol 15: 924

Released	2008-08-19
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Homo sapiens
Macromolecule	PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA (protein)
Unique Ligands	9HO

Explore in 3D

2VST \| pdb_00002vst	Download File View File

hPPARgamma Ligand binding domain in complex with 13-(S)-HODE

Itoh, T., Fairall, L., Schwabe, J.W.R.

(2008) Nat Struct Mol Biol 15: 924

Released	2008-08-19
Method	X-RAY DIFFRACTION 2.35 Å
Organisms	Homo sapiens
Macromolecule	PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA (protein)
Unique Ligands	243

Explore in 3D

2VV0 \| pdb_00002vv0	Download File View File

hPPARgamma Ligand binding domain in complex with DHA

Itoh, T., Fairall, L., Schwabe, J.W.R.

(2008) Nat Struct Mol Biol 15: 924

Released	2008-08-19
Method	X-RAY DIFFRACTION 2.55 Å
Organisms	Homo sapiens
Macromolecule	PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA (protein)
Unique Ligands	HXA

Explore in 3D

2VV1 \| pdb_00002vv1	Download File View File

hPPARgamma Ligand binding domain in complex with 4-HDHA

Itoh, T., Fairall, L., Schwabe, J.W.R.

(2008) Nat Struct Mol Biol 15: 924

Released	2008-08-19
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA (protein)
Unique Ligands	4HD

Explore in 3D

2VV2 \| pdb_00002vv2	Download File View File

hPPARgamma Ligand binding domain in complex with 5-HEPA

Itoh, T., Fairall, L., Schwabe, J.W.R.

(2008) Nat Struct Mol Biol 15: 924

Released	2008-08-19
Method	X-RAY DIFFRACTION 2.75 Å
Organisms	Homo sapiens
Macromolecule	PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA (protein)
Unique Ligands	5HE

Explore in 3D

2VV3 \| pdb_00002vv3	Download File View File

hPPARgamma Ligand binding domain in complex with 4-oxoDHA

Itoh, T., Fairall, L., Schwabe, J.W.R.

(2008) Nat Struct Mol Biol 15: 924

Released	2008-08-19
Method	X-RAY DIFFRACTION 2.85 Å
Organisms	Homo sapiens
Macromolecule	PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA (protein)
Unique Ligands	4R8

Explore in 3D

2VV4 \| pdb_00002vv4	Download File View File

hPPARgamma Ligand binding domain in complex with 6-oxoOTE

Itoh, T., Fairall, L., Schwabe, J.W.R.

(2008) Nat Struct Mol Biol 15: 924

Released	2008-08-19
Method	X-RAY DIFFRACTION 2.35 Å
Organisms	Homo sapiens
Macromolecule	PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA (protein)
Unique Ligands	6OB, 6OC

Explore in 3D

2XTC \| pdb_00002xtc	Download File View File

Structure of the TBL1 tetramerisation domain

Oberoi, J., Fairall, L., Watson, P.J., Greenwood, J.A., Schwabe, J.W.R.

(2011) Nat Struct Mol Biol 18: 177

Released	2011-01-19
Method	X-RAY DIFFRACTION 2.22 Å
Organisms	Homo sapiens
Macromolecule	F-BOX-LIKE/WD REPEAT-CONTAINING PROTEIN TBL1X (protein)

Explore in 3D

2XTD \| pdb_00002xtd	Download File View File

Structure of the TBL1 tetramerisation domain

Oberoi, J., Fairall, L., Watson, P.J., Greenwood, J.A., Schwabe, J.W.R.

(2011) Nat Struct Mol Biol 18: 177

Released	2011-01-19
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Homo sapiens
Macromolecule	TBL1 F-BOX-LIKE/WD REPEAT-CONTAINING PROTEIN TBL1X (protein)

Explore in 3D

2XTE \| pdb_00002xte	Download File View File

Structure of the TBL1 tetramerisation domain

Oberoi, J., Fairall, L., Watson, P.J., Greenwood, J.A., Schwabe, J.W.R.

(2011) Nat Struct Mol Biol 18: 177

Released	2011-01-19
Method	X-RAY DIFFRACTION 3.9 Å
Organisms	Homo sapiens
Macromolecule	F-BOX-LIKE/WD REPEAT-CONTAINING PROTEIN TBL1X (protein)

Explore in 3D

2YHN \| pdb_00002yhn	Download File View File

The IDOL-UBE2D complex mediates sterol-dependent degradation of the LDL receptor

Fairall, L., Goult, B.T., Millard, C.J., Tontonoz, P., Schwabe, J.W.R.

(2011) Genes Dev 25: 1262

Released	2011-06-29
Method	X-RAY DIFFRACTION 3 Å
Organisms	Homo sapiens
Macromolecule	E3 UBIQUITIN-PROTEIN LIGASE MYLIP (protein)
Unique Ligands	ZN

Explore in 3D

2YHO \| pdb_00002yho	Download File View File

The IDOL-UBE2D complex mediates sterol-dependent degradation of the LDL receptor

Fairall, L., Goult, B.T., Millard, C.J., Tontonoz, P., Schwabe, J.W.R.

(2011) Genes Dev 25: 1262

Released	2011-06-29
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	E3 UBIQUITIN-PROTEIN LIGASE MYLIP (protein) UBIQUITIN-CONJUGATING ENZYME E2 D1 (protein)
Unique Ligands	ACT, ZN

Explore in 3D

4A69 \| pdb_00004a69	Download File View File

Structure of HDAC3 bound to corepressor and inositol tetraphosphate

Watson, P.J., Fairall, L., Santos, G.M., Schwabe, J.W.R.

(2012) Nature 481: 335

Released	2012-01-11
Method	X-RAY DIFFRACTION 2.06 Å
Organisms	Homo sapiens
Macromolecule	HISTONE DEACETYLASE 3, (protein) NUCLEAR RECEPTOR COREPRESSOR 2 (protein)
Unique Ligands	ACT, GOL, I0P, K, ZN

Explore in 3D

4BKX \| pdb_00004bkx	Download File View File

The structure of HDAC1 in complex with the dimeric ELM2-SANT domain of MTA1 from the NuRD complex

Millard, C.J., Watson, P.J., Celardo, I., Gordiyenko, Y., Cowley, S.M., Robinson, C.V., Fairall, L., Schwabe, J.W.R.

(2013) Mol Cell 51: 57

Released	2013-07-03
Method	X-RAY DIFFRACTION 3 Å
Organisms	Homo sapiens
Macromolecule	HISTONE DEACETYLASE 1 (protein) METASTASIS-ASSOCIATED PROTEIN MTA1 (protein)
Unique Ligands	ACT, K, SO4, ZN

Explore in 3D

4CP3 \| pdb_00004cp3	Download File View File

The structure of BCL6 BTB (POZ) domain in complex with the ansamycin antibiotic rifabutin.

Evans, S.E., Fairall, L., Goult, B.T., Jamieson, A.G., Ferrigno, P.K., Ford, R., Wagner, S.D., Schwabe, J.W.R.

(2014) PLoS One 9: 90889

Released	2014-03-19
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	B-CELL LYMPHOMA 6 PROTEIN (protein)
Unique Ligands	RBT

Explore in 3D

4D6K \| pdb_00004d6k	Download File View File

Structure of DNTTIP1 dimerisation domain.

Itoh, T., Fairall, L., Schwabe, J.W.R.

(2015) Nucleic Acids Res 43: 2033

Released	2015-02-18
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	DEOXYNUCLEOTIDYLTRANSFERASE TERMINAL-INTERACTING PROTEIN 1 (protein)

1 to 25 of 37 Structures

Page 1 of 2

Sort by

About
About Us
Citing Us
Publications
Team
Careers
Usage & Privacy

Support
Contact Us
Help
Website FAQ
Glossary
Service Status

RCSB PDB is hosted by

RCSB PDB is a member of the

RCSB Partners
Nucleic Acid Knowledgebase

wwPDB Partners
RCSB PDB
PDBe
PDBj
BMRB
EMDB

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

Prepare Data

Validate Data

Deposit Data

Help and Resources

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

1H9U | pdb_00001h9u

1HCP | pdb_00001hcp

1HCQ | pdb_00001hcq

1HG4 | pdb_00001hg4

1XC5 | pdb_00001xc5

1ZFD | pdb_00001zfd

2DRP | pdb_00002drp

2L5G | pdb_00002l5g

2MWI | pdb_00002mwi

2VSR | pdb_00002vsr

2VST | pdb_00002vst

2VV0 | pdb_00002vv0

2VV1 | pdb_00002vv1

2VV2 | pdb_00002vv2

2VV3 | pdb_00002vv3

2VV4 | pdb_00002vv4

2XTC | pdb_00002xtc

2XTD | pdb_00002xtd

2XTE | pdb_00002xte

2YHN | pdb_00002yhn

2YHO | pdb_00002yho

4A69 | pdb_00004a69

4BKX | pdb_00004bkx

4CP3 | pdb_00004cp3

4D6K | pdb_00004d6k