7O04 | pdb_00007o04

Crystal structure of a shortened IpgC variant in complex with [(2-chloro-5-nitrophenyl)methyl](methyl)amine

PDB DOI: https://doi.org/10.2210/pdb7O04/pdb

Classification: CHAPERONE
Organism(s): Shigella flexneri
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-03-25 Released: 2022-04-13
Deposition Author(s): Gardonyi, M., Heine, A., Klebe, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free:
0.220 (Depositor), 0.220 (DCC)
R-Value Work:
0.178 (Depositor), 0.180 (DCC)
R-Value Observed:
0.180 (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

Crystal structure of a shortened IpgC variant in complex with [(2-chloro-5-nitrophenyl)methyl](methyl)amine

Gardonyi, M., Heine, A., Klebe, G.

To be published.

Macromolecule Content

Total Structure Weight: 33.25 kDa
Atom Count: 2,424
Modeled Residue Count: 273
Deposited Residue Count: 286
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chaperone protein IpgC	A, B	143	Shigella flexneri	Mutation(s): 0 Gene Names: ipgC, ippI, CP0129
UniProt
Find proteins for P0A2U4 (Shigella flexneri) Explore P0A2U4 Go to UniProtKB: P0A2U4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A2U4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4AV Query on 4AV Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	1-(2-chloro-5-nitrophenyl)-N-methylmethanamine C₈ H₉ Cl N₂ O₂ YRTNCUPHKWUHMQ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain H [auth A]	H [auth A], L [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Interactions & Density Focus chain H [auth A] Focus chain L [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], J [auth B], K [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain I [auth B]