9IQD | pdb_00009iqd

Apo-MicM,homologous of AkaM, SnoaL-like protein

PDB DOI: https://doi.org/10.2210/pdb9IQD/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Micromonospora sp. HM134
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2024-07-12 Released: 2025-07-16
Deposition Author(s): Zhang, B., Ge, H.M.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free:
0.216 (Depositor), 0.216 (DCC)
R-Value Work:
0.181 (Depositor), 0.181 (DCC)
R-Value Observed:
0.183 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Tandem Michael addition and Knoevenagel condensation catalyzed by NTF2-Like Enzymes as iminium catalysis

Liu, C.L., Zhang, B., Ge, H.M.

To be published.

Macromolecule Content

Total Structure Weight: 59.15 kDa
Atom Count: 4,233
Modeled Residue Count: 477
Deposited Residue Count: 528
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SnoaL-like domain-containing protein	A, B, C, D	132	Micromonospora sp. HM134	Mutation(s): 0 Gene Names: FJK98_13695
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain N [auth C] MOL2 format, chain N [auth C] mmCIF format, chain N [auth C]	N [auth C]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain N [auth C] Interactions & Density Focus chain N [auth C]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain O [auth C] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain O [auth C] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain O [auth C]	G [auth A], J [auth B], O [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain O [auth C] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain O [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain I [auth B] SDF format, chain K [auth B] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain P [auth C] SDF format, chain R [auth D] SDF format, chain S [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain P [auth C] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C] mmCIF format, chain P [auth C] mmCIF format, chain R [auth D] mmCIF format, chain S [auth D]	E [auth A] F [auth A] H [auth A] I [auth B] K [auth B] E [auth A], F [auth A], H [auth A], I [auth B], K [auth B], L [auth C], M [auth C], P [auth C], R [auth D], S [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain P [auth C] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain P [auth C] Focus chain R [auth D] Focus chain S [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain Q [auth C] SDF format, chain T [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain T [auth D]	Q [auth C], T [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain Q [auth C] Focus chain T [auth D] Interactions & Density Focus chain Q [auth C] Focus chain T [auth D]