8XXC | pdb_00008xxc

DaCS-intermediate complex

PDB DOI: https://doi.org/10.2210/pdb8XXC/pdb

Classification: TRANSFERASE
Organism(s): Desulfurella acetivorans A63
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-01-18 Released: 2025-01-22
Deposition Author(s): Yang, L., Fang, Y.J.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free:
0.239 (Depositor), 0.246 (DCC)
R-Value Work:
0.196 (Depositor), 0.204 (DCC)
R-Value Observed:
0.198 (Depositor)

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

DaCS-intermediate complex

Yang, L., Fang, Y.J.

To be published.

Macromolecule Content

Total Structure Weight: 392.82 kDa
Atom Count: 29,531
Modeled Residue Count: 3,475
Deposited Residue Count: 3,480
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Citrate synthase	A, B, C, D, E A, B, C, D, E, F, G, H	435	Desulfurella acetivorans A63	Mutation(s): 0 EC: 2.3.3.16
UniProt
Find proteins for A0A7C6A739 (Desulfurella acetivorans) Explore A0A7C6A739 Go to UniProtKB: A0A7C6A739
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A7C6A739
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT (Subject of Investigation/LOI) Query on CIT Download Ideal Coordinates CCD File SDF format, chain Q [auth G] SDF format, chain R [auth H] SDF format, chain L [auth D] SDF format, chain K [auth C] SDF format, chain J [auth B] SDF format, chain I [auth A] MOL2 format, chain Q [auth G] MOL2 format, chain R [auth H] MOL2 format, chain L [auth D] MOL2 format, chain K [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth A] mmCIF format, chain Q [auth G] mmCIF format, chain R [auth H] mmCIF format, chain L [auth D] mmCIF format, chain K [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth A]	I [auth A] J [auth B] K [auth C] L [auth D] Q [auth G] I [auth A], J [auth B], K [auth C], L [auth D], Q [auth G], R [auth H]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain Q [auth G] Focus chain R [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain Q [auth G] Focus chain R [auth H]
OAA (Subject of Investigation/LOI) Query on OAA Download Ideal Coordinates CCD File SDF format, chain P [auth F] SDF format, chain N [auth E] MOL2 format, chain P [auth F] MOL2 format, chain N [auth E] mmCIF format, chain P [auth F] mmCIF format, chain N [auth E]	N [auth E], P [auth F]	OXALOACETATE ION C₄ H₃ O₅ KHPXUQMNIQBQEV-UHFFFAOYSA-M		Interactions Focus chain N [auth E] Focus chain P [auth F] Interactions & Density Focus chain N [auth E] Focus chain P [auth F]
ACY (Subject of Investigation/LOI) Query on ACY Download Ideal Coordinates CCD File SDF format, chain M [auth E] SDF format, chain O [auth F] MOL2 format, chain M [auth E] MOL2 format, chain O [auth F] mmCIF format, chain M [auth E] mmCIF format, chain O [auth F]	M [auth E], O [auth F]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain M [auth E] Focus chain O [auth F] Interactions & Density Focus chain M [auth E] Focus chain O [auth F]