8BAI | pdb_00008bai

The surface-exposed lipo-protein of BtuG2 in complex with cyanocobalamin.

PDB DOI: https://doi.org/10.2210/pdb8BAI/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Bacteroides thetaiotaomicron
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-10-11 Released: 2023-10-25
Deposition Author(s): Whittaker, J., Martinez Felices, J.M., Guskov, A., Slotboom, D.J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.69 Å
R-Value Free:
0.180 (Depositor), 0.183 (DCC)
R-Value Work:
0.157 (Depositor), 0.157 (DCC)
R-Value Observed:
0.157 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

The surface-exposed lipo-protein of BtuG2 in complex with cyanocobalamin.

Whittaker, J., Guskov, A.

To be published.

Macromolecule Content

Total Structure Weight: 156.54 kDa
Atom Count: 11,812
Modeled Residue Count: 1,282
Deposited Residue Count: 1,284
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Surface layer protein	A, B, C, D	321	Bacteroides thetaiotaomicron	Mutation(s): 0 Gene Names: BT_1954
UniProt
Find proteins for Q8A6D0 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A6D0 Go to UniProtKB: Q8A6D0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8A6D0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CNC Query on CNC Download:Ideal Coordinates CCD File SDF format, chain GA [auth D] SDF format, chain L [auth A] SDF format, chain T [auth B] SDF format, chain AA [auth C] MOL2 format, chain GA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain T [auth B] MOL2 format, chain AA [auth C] mmCIF format, chain GA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain T [auth B] mmCIF format, chain AA [auth C]	AA [auth C], GA [auth D], L [auth A], T [auth B]	CYANOCOBALAMIN C₆₃ H₈₉ Co N₁₄ O₁₄ P SYZBZQWSWIJYAR-UVKKECPRSA-M		Interactions Focus chain AA [auth C] Focus chain GA [auth D] Focus chain L [auth A] Focus chain T [auth B] Interactions & Density Focus chain AA [auth C] Focus chain GA [auth D] Focus chain L [auth A] Focus chain T [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain Y [auth C] MOL2 format, chain U [auth B] MOL2 format, chain Y [auth C] mmCIF format, chain U [auth B] mmCIF format, chain Y [auth C]	U [auth B], Y [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain U [auth B] Focus chain Y [auth C] Interactions & Density Focus chain U [auth B] Focus chain Y [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain Z [auth C] MOL2 format, chain S [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain S [auth B] mmCIF format, chain Z [auth C]	S [auth B], Z [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain S [auth B] Focus chain Z [auth C] Interactions & Density Focus chain S [auth B] Focus chain Z [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain F [auth A] SDF format, chain FA [auth D] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain V [auth C] SDF format, chain X [auth C] SDF format, chain W [auth C] SDF format, chain M [auth B] SDF format, chain J [auth A] SDF format, chain G [auth A] SDF format, chain E [auth A] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain V [auth C] MOL2 format, chain X [auth C] MOL2 format, chain W [auth C] MOL2 format, chain M [auth B] MOL2 format, chain J [auth A] MOL2 format, chain G [auth A] MOL2 format, chain E [auth A] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain V [auth C] mmCIF format, chain X [auth C] mmCIF format, chain W [auth C] mmCIF format, chain M [auth B] mmCIF format, chain J [auth A] mmCIF format, chain G [auth A] mmCIF format, chain E [auth A]	BA [auth D] CA [auth D] DA [auth D] E [auth A] EA [auth D] BA [auth D], CA [auth D], DA [auth D], E [auth A], EA [auth D], F [auth A], FA [auth D], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], V [auth C], W [auth C], X [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain E [auth A] Focus chain EA [auth D] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain E [auth A] Focus chain EA [auth D] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain IA [auth D] SDF format, chain HA [auth D] MOL2 format, chain IA [auth D] MOL2 format, chain HA [auth D] mmCIF format, chain IA [auth D] mmCIF format, chain HA [auth D]	HA [auth D], IA [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain HA [auth D] Focus chain IA [auth D] Interactions & Density Focus chain HA [auth D] Focus chain IA [auth D]