9ERQ | pdb_00009erq

Citramalate lyase - AMPPNP- citramalate complex

PDB DOI: https://doi.org/10.2210/pdb9ERQ/pdb

Classification: LYASE
Organism(s): Klebsiella michiganensis
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2024-03-25 Released: 2025-10-22
Deposition Author(s): Ermler, U., Berg, I.A., Demmer, U.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free:
0.185 (Depositor), 0.185 (DCC)
R-Value Work:
0.163 (Depositor), 0.163 (DCC)
R-Value Observed:
0.164 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Novel citramalate lyase involved in glutamate fermentation of enterobacteria

Eggers, J., Schaefer, L., Cassens, E.A., Schmid, L., Simon, S.A., Probst, A.J., Koenig, S., Demmer, U., Ermler, U., Berg, I.A.

To be published.

Macromolecule Content

Total Structure Weight: 124.09 kDa
Atom Count: 9,993
Modeled Residue Count: 1,122
Deposited Residue Count: 1,122
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyclic terpene utilization AtuA family protein	A, C	456	Klebsiella michiganensis	Mutation(s): 0 Gene Names: CWM85_18250, CWN49_12110, PTQ40_16850
UniProt
Find proteins for A0A2K0K9V8 (Klebsiella michiganensis) Explore A0A2K0K9V8 Go to UniProtKB: A0A2K0K9V8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2K0K9V8
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DUF4387 domain-containing protein	B, D	105	Klebsiella michiganensis	Mutation(s): 0 Gene Names: CWN49_12105, GW952_12775, L373_04358
UniProt
Find proteins for A0A249WD43 (Klebsiella michiganensis) Explore A0A249WD43 Go to UniProtKB: A0A249WD43
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A249WD43
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP Query on ANP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain M [auth C] MOL2 format, chain E [auth A] MOL2 format, chain M [auth C] mmCIF format, chain E [auth A] mmCIF format, chain M [auth C]	E [auth A], M [auth C]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain M [auth C] Interactions & Density Focus chain E [auth A] Focus chain M [auth C]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain R [auth C] MOL2 format, chain J [auth A] MOL2 format, chain R [auth C] mmCIF format, chain J [auth A] mmCIF format, chain R [auth C]	J [auth A], R [auth C]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain R [auth C] Interactions & Density Focus chain J [auth A] Focus chain R [auth C]
S2G Query on S2G Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain S [auth D] MOL2 format, chain L [auth B] MOL2 format, chain S [auth D] mmCIF format, chain L [auth B] mmCIF format, chain S [auth D]	L [auth B], S [auth D]	(2S)-2-HYDROXYPENTANEDIOIC ACID C₅ H₈ O₅ HWXBTNAVRSUOJR-VKHMYHEASA-N		Interactions Focus chain L [auth B] Focus chain S [auth D] Interactions & Density Focus chain L [auth B] Focus chain S [auth D]
A1H6S (Subject of Investigation/LOI) Query on A1H6S Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain Q [auth C] MOL2 format, chain I [auth A] MOL2 format, chain Q [auth C] mmCIF format, chain I [auth A] mmCIF format, chain Q [auth C]	I [auth A], Q [auth C]	(2~{S})-2-methyl-2-oxidanyl-butanedioic acid C₅ H₈ O₅ XFTRTWQBIOMVPK-YFKPBYRVSA-N		Interactions Focus chain I [auth A] Focus chain Q [auth C] Interactions & Density Focus chain I [auth A] Focus chain Q [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain P [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C]	F [auth A] G [auth A] H [auth A] N [auth C] O [auth C] F [auth A], G [auth A], H [auth A], N [auth C], O [auth C], P [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C]