9D5W

Crystal Structure of the Substrate Binding Domain Protein of the ABC Transporter PBP2_YxeM from Vibrio cholerae

PDB DOI: https://doi.org/10.2210/pdb9D5W/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-08-14 Released: 2024-08-28
Deposition Author(s): Kim, Y., Maltseva, N., Grimshaw, S., Joachimiak, A., Center for Structural Biology of Infectious Diseases (CSBID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.229
R-Value Work: 0.194

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

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

Literature

Crystal Structure of the Substrate Binding Domain Protein of the ABC Transporter PBP2_YxeM from Vibrio cholerae

Kim, Y., Maltseva, N., Grimshaw, S., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 232.84 kDa
Atom Count: 16,666
Modelled Residue Count: 2,043
Deposited Residue Count: 2,097
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amino acid ABC transporter, periplasmic amino acid-binding portion	A, B, C, D, E A, B, C, D, E, F, G, H, I	233	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0 Gene Names: VC_0010
UniProt
Find proteins for Q9KVX8 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KVX8 Go to UniProtKB: Q9KVX8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9KVX8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain JA [auth G] SDF format, chain KA [auth G] MOL2 format, chain AA [auth D] MOL2 format, chain JA [auth G] MOL2 format, chain KA [auth G]	AA [auth D], JA [auth G], KA [auth G]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth D] Focus chain JA [auth G] Focus chain KA [auth G]
PGR Query on PGR Download Ideal Coordinates CCD File SDF format, chain T [auth C] MOL2 format, chain T [auth C]	T [auth C]	R-1,2-PROPANEDIOL C₃ H₈ O₂ DNIAPMSPPWPWGF-GSVOUGTGSA-N		Interactions Focus chain T [auth C]
PGO Query on PGO Download Ideal Coordinates CCD File SDF format, chain IA [auth G] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain QA [auth I] SDF format, chain X [auth D] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain IA [auth G] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain QA [auth I] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D]	IA [auth G] J [auth A] K [auth A] O [auth B] P [auth B] IA [auth G], J [auth A], K [auth A], O [auth B], P [auth B], QA [auth I], X [auth D], Y [auth D], Z [auth D]	S-1,2-PROPANEDIOL C₃ H₈ O₂ DNIAPMSPPWPWGF-VKHMYHEASA-N		Interactions Focus chain IA [auth G] Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain QA [auth I] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D]
K Query on K Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain DA [auth E] SDF format, chain N [auth A] SDF format, chain NA [auth G] SDF format, chain S [auth B] SDF format, chain W [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain DA [auth E] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth G] MOL2 format, chain S [auth B] MOL2 format, chain W [auth C]	BA [auth D] DA [auth E] N [auth A] NA [auth G] S [auth B] BA [auth D], DA [auth E], N [auth A], NA [auth G], S [auth B], W [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain DA [auth E] Focus chain N [auth A] Focus chain NA [auth G] Focus chain S [auth B] Focus chain W [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain EA [auth F] SDF format, chain FA [auth F] SDF format, chain GA [auth F] SDF format, chain HA [auth F] SDF format, chain L [auth A] SDF format, chain LA [auth G] SDF format, chain M [auth A] SDF format, chain MA [auth G] SDF format, chain OA [auth H] SDF format, chain PA [auth H] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain RA [auth I] SDF format, chain SA [auth I] SDF format, chain U [auth C] SDF format, chain V [auth C] MOL2 format, chain CA [auth E] MOL2 format, chain EA [auth F] MOL2 format, chain FA [auth F] MOL2 format, chain GA [auth F] MOL2 format, chain HA [auth F] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth G] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth G] MOL2 format, chain OA [auth H] MOL2 format, chain PA [auth H] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth I] MOL2 format, chain SA [auth I] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C]	CA [auth E] EA [auth F] FA [auth F] GA [auth F] HA [auth F] CA [auth E], EA [auth F], FA [auth F], GA [auth F], HA [auth F], L [auth A], LA [auth G], M [auth A], MA [auth G], OA [auth H], PA [auth H], Q [auth B], R [auth B], RA [auth I], SA [auth I], U [auth C], V [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain CA [auth E] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain L [auth A] Focus chain LA [auth G] Focus chain M [auth A] Focus chain MA [auth G] Focus chain OA [auth H] Focus chain PA [auth H] Focus chain Q [auth B] Focus chain R [auth B] Focus chain RA [auth I] Focus chain SA [auth I] Focus chain U [auth C] Focus chain V [auth C]