8PTF | pdb_00008ptf

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

PDB DOI: https://doi.org/10.2210/pdb8PTF/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Bacteroides thetaiotaomicron
Expression System: Escherichia coli BL21(DE3)
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: 1.95 Å
R-Value Free:
0.281 (Depositor), 0.280 (DCC)
R-Value Work:
0.235 (Depositor), 0.240 (DCC)
R-Value Observed:
0.237 (Depositor)

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 cyanocobinamide.

Whittaker, J., Guskov, A.

To be published.

Macromolecule Content

Total Structure Weight: 38.96 kDa
Atom Count: 2,869
Modeled Residue Count: 342
Deposited Residue Count: 342
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YncE family protein	A	342	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CBY Query on CBY Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	COB(II)INAMIDE C₄₈ H₇₂ Co N₁₁ O₈ GFVWZOGCSKVPRA-JFYQDRLCSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
3P8 Query on 3P8 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	methylammonium ion C H₆ N BAVYZALUXZFZLV-UHFFFAOYSA-O		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A]	H [auth A] I [auth A] J [auth A] K [auth A] L [auth A] H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A]