7XJM | pdb_00007xjm

Structure of VcPotD1 in complex with spermidine

PDB DOI: https://doi.org/10.2210/pdb7XJM/pdb

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

Deposited: 2022-04-18 Released: 2023-04-26
Deposition Author(s): Ma, Q., Liu, C.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.201 (Depositor), 0.202 (DCC)
R-Value Work:
0.183 (Depositor), 0.184 (DCC)
R-Value Observed:
0.184 (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

structure of VcPotD1 in complex with spermidine

Ma, Q., Liu, C.

To be published.

Macromolecule Content

Total Structure Weight: 149.49 kDa
Atom Count: 11,178
Modeled Residue Count: 1,281
Deposited Residue Count: 1,304
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putrescine-binding periplasmic protein	A, B, C, D	326	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0 Gene Names: VC_1424
UniProt
Find proteins for Q9KS37 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KS37 Go to UniProtKB: Q9KS37
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KS37
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P6G Query on P6G Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth C] MOL2 format, chain F [auth A] MOL2 format, chain I [auth C] mmCIF format, chain F [auth A] mmCIF format, chain I [auth C]	F [auth A], I [auth C]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth C] Interactions & Density Focus chain F [auth A] Focus chain I [auth C]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain K [auth D] MOL2 format, chain K [auth D] mmCIF format, chain K [auth D]	K [auth D]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain K [auth D] Interactions & Density Focus chain K [auth D]
SPD (Subject of Investigation/LOI) Query on SPD Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth C] SDF format, chain J [auth D] SDF format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth C] MOL2 format, chain J [auth D] MOL2 format, chain G [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth C] mmCIF format, chain J [auth D] mmCIF format, chain G [auth B]	E [auth A], G [auth B], H [auth C], J [auth D]	SPERMIDINE C₇ H₁₉ N₃ ATHGHQPFGPMSJY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth C] Focus chain J [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth C] Focus chain J [auth D]