4HPE

Crystal structure of a putative cell wall hydrolase (CD630_03720) from Clostridium difficile 630 at 2.38 A resolution

PDB DOI: https://doi.org/10.2210/pdb4HPE/pdb

Classification: HYDROLASE
Organism(s): Clostridioides difficile 630
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-10-23 Released: 2012-11-28
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Free: 0.211
R-Value Work: 0.175
R-Value Observed: 0.176

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of a putative cell wall hydrolase (CD630_03720) from Clostridium difficile 630 at 2.38 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 203.84 kDa
Atom Count: 13,970
Modelled Residue Count: 1,735
Deposited Residue Count: 1,848
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative cell wall hydrolase Tn916-like,CTn1-Orf17	A, B, C, D, E A, B, C, D, E, F	308	Clostridioides difficile 630	Mutation(s): 0 Gene Names: CD630_03720, YP_001086839.1
UniProt
Find proteins for Q18DB2 (Clostridioides difficile (strain 630)) Explore Q18DB2 Go to UniProtKB: Q18DB2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q18DB2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain N [auth B] SDF format, chain Q [auth D] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth D] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth D]	K [auth A], L [auth A], N [auth B], Q [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth B] Focus chain Q [auth D] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth B] Focus chain Q [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain O [auth C] SDF format, chain P [auth D] SDF format, chain R [auth E] SDF format, chain S [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth D] MOL2 format, chain R [auth E] MOL2 format, chain S [auth F] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain O [auth C] mmCIF format, chain P [auth D] mmCIF format, chain R [auth E] mmCIF format, chain S [auth F]	G [auth A] H [auth A] I [auth A] J [auth A] M [auth B] G [auth A], H [auth A], I [auth A], J [auth A], M [auth B], O [auth C], P [auth D], R [auth E], S [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain S [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain S [auth F]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET
OCS Query on OCS	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₃ H₇ N O₅ S		CYS