8PTD

The surface-exposed lipo-protein of BtuG1 in complex with cyanocobalamin.

PDB DOI: https://doi.org/10.2210/pdb8PTD/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Bacteroides thetaiotaomicron
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-07-14 Released: 2024-07-24
Deposition Author(s): Whittaker, J., Felices Martinez, J.M., Guskov, A., Slotboom, D.J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.192
R-Value Work: 0.172
R-Value Observed: 0.173

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

The surface-exposed lipo-protein of BtuG1 in complex with cyanocobalamin.

Whittaker, J., Guskov, A.

To be published.

Macromolecule Content

Total Structure Weight: 39.38 kDa
Atom Count: 3,052
Modelled Residue Count: 343
Deposited Residue Count: 343
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YncE family protein	A	343	Bacteroides thetaiotaomicron	Mutation(s): 0 Gene Names: BT_1490
UniProt
Find proteins for Q8A7N4 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A7N4 Go to UniProtKB: Q8A7N4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8A7N4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B12 Query on B12 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	COBALAMIN C₆₂ H₈₉ Co N₁₃ O₁₄ P LKVIQTCSMMVGFU-DWSMJLPVSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain E [auth A] MOL2 format, chain B [auth A] MOL2 format, chain E [auth A] mmCIF format, chain B [auth A] mmCIF format, chain E [auth A]	B [auth A], E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain E [auth A] Interactions & Density Focus chain B [auth A] Focus chain E [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	F [auth A], G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
OH Query on OH Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	HYDROXIDE ION H O XLYOFNOQVPJJNP-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]