9WLV | pdb_00009wlv

The Crystal Structure of Alpha-Beta-fold_hydrolase from Microlunatus sagamiharensis.

PDB DOI: https://doi.org/10.2210/pdb9WLV/pdb

Classification: HYDROLASE
Organism(s): Microlunatus sagamiharensis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-09-02 Released: 2025-10-29
Deposition Author(s): Huang, J., Smith, S., Wang, Q., Bao, X.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.179 (Depositor), 0.192 (DCC)
R-Value Work:
0.144 (Depositor), 0.157 (DCC)

Starting Model: in silico
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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

The Crystal Structure of Alpha-Beta-fold_hydrolase from Microlunatus sagamiharensis.

Huang, J., Smith, S., Wang, Q., Bao, X.

To be published.

Macromolecule Content

Total Structure Weight: 61.79 kDa
Atom Count: 5,003
Modeled Residue Count: 580
Deposited Residue Count: 580
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pimeloyl-ACP methyl ester carboxylesterase	A [auth AAA], B [auth BBB]	290	Microlunatus sagamiharensis	Mutation(s): 0 Gene Names: SAMN04488544_1883
UniProt
Find proteins for A0A1H2MDS2 (Microlunatus sagamiharensis) Explore A0A1H2MDS2 Go to UniProtKB: A0A1H2MDS2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1H2MDS2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4HP Query on 4HP Download Ideal Coordinates CCD File SDF format, chain M [auth BBB] SDF format, chain F [auth AAA] MOL2 format, chain M [auth BBB] MOL2 format, chain F [auth AAA] mmCIF format, chain M [auth BBB] mmCIF format, chain F [auth AAA]	F [auth AAA], M [auth BBB]	4-HYDROXYPHENYLACETATE C₈ H₈ O₃ XQXPVVBIMDBYFF-UHFFFAOYSA-N		Interactions Focus chain F [auth AAA] Focus chain M [auth BBB] Interactions & Density Focus chain F [auth AAA] Focus chain M [auth BBB]
3HR Query on 3HR Download Ideal Coordinates CCD File SDF format, chain O [auth BBB] MOL2 format, chain O [auth BBB] mmCIF format, chain O [auth BBB]	O [auth BBB]	(3R)-3-hydroxybutanoic acid C₄ H₈ O₃ WHBMMWSBFZVSSR-GSVOUGTGSA-N		Interactions Focus chain O [auth BBB] Interactions & Density Focus chain O [auth BBB]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth AAA] SDF format, chain C [auth AAA] MOL2 format, chain D [auth AAA] MOL2 format, chain C [auth AAA] mmCIF format, chain D [auth AAA] mmCIF format, chain C [auth AAA]	C [auth AAA], D [auth AAA]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth AAA] Focus chain D [auth AAA] Interactions & Density Focus chain C [auth AAA] Focus chain D [auth AAA]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain P [auth BBB] SDF format, chain N [auth BBB] SDF format, chain L [auth AAA] SDF format, chain K [auth AAA] SDF format, chain J [auth AAA] SDF format, chain I [auth AAA] SDF format, chain H [auth AAA] SDF format, chain G [auth AAA] MOL2 format, chain P [auth BBB] MOL2 format, chain N [auth BBB] MOL2 format, chain L [auth AAA] MOL2 format, chain K [auth AAA] MOL2 format, chain J [auth AAA] MOL2 format, chain I [auth AAA] MOL2 format, chain H [auth AAA] MOL2 format, chain G [auth AAA] mmCIF format, chain P [auth BBB] mmCIF format, chain N [auth BBB] mmCIF format, chain L [auth AAA] mmCIF format, chain K [auth AAA] mmCIF format, chain J [auth AAA] mmCIF format, chain I [auth AAA] mmCIF format, chain H [auth AAA] mmCIF format, chain G [auth AAA]	G [auth AAA] H [auth AAA] I [auth AAA] J [auth AAA] K [auth AAA] G [auth AAA], H [auth AAA], I [auth AAA], J [auth AAA], K [auth AAA], L [auth AAA], N [auth BBB], P [auth BBB]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain J [auth AAA] Focus chain K [auth AAA] Focus chain L [auth AAA] Focus chain N [auth BBB] Focus chain P [auth BBB] Interactions & Density Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain J [auth AAA] Focus chain K [auth AAA] Focus chain L [auth AAA] Focus chain N [auth BBB] Focus chain P [auth BBB]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain E [auth AAA] MOL2 format, chain E [auth AAA] mmCIF format, chain E [auth AAA]	E [auth AAA]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth AAA] Interactions & Density Focus chain E [auth AAA]