9L5O | pdb_00009l5o

Crystal structure of the mutant Y549A of collagenase VhaC

PDB DOI: https://doi.org/10.2210/pdb9L5O/pdb

Classification: HYDROLASE
Organism(s): Vibrio harveyi VHJR7
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-12-23 Released: 2025-11-05
Deposition Author(s): Zhao, W.X.
Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.221 (Depositor), 0.222 (DCC)
R-Value Work:
0.178 (Depositor), 0.179 (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 1.0 of the entry. See complete history.

Literature

Crystal structure of the mutant Y549A of collagenase VhaC

Zhao, W.X.

To be published.

Macromolecule Content

Total Structure Weight: 64.52 kDa
Atom Count: 5,043
Modeled Residue Count: 565
Deposited Residue Count: 565
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
microbial collagenase	A	532	Vibrio harveyi VHJR7	Mutation(s): 1 Gene Names: DS957_010145 EC: 3.4.24.3
UniProt
Find proteins for A0A8B3DGT3 (Vibrio harveyi) Explore A0A8B3DGT3 Go to UniProtKB: A0A8B3DGT3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A8B3DGT3
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LEU-SER-GLU-PRO-SER-GLN-GLN-VAL-THR-GLU-ILE-TYR-GLN-HIS-HIS-ALA-HIS-GLN-ASN-GLY-ASN	B	21	Vibrio harveyi VHJR7	Mutation(s): 0
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Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ASP-TYR-ALA-PRO-THR-LYS-LEU-LEU-PRO-GLN-GLN-PRO	C	12	Vibrio harveyi VHJR7	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL (Subject of Investigation/LOI) Query on GOL Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain O [auth A] MOL2 format, chain O [auth A] mmCIF format, chain O [auth A]	O [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Interactions & Density Focus chain O [auth A]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A]	L [auth A], M [auth A], N [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A]