6Z2H | pdb_00006z2h

Citryl-CoA lyase module of human ATP citrate lyase in complex with (3S)-citryl-CoA.

PDB DOI: https://doi.org/10.2210/pdb6Z2H/pdb

Classification: LYASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-05-15 Released: 2021-05-26
Deposition Author(s): Verschueren, K.H.G., Verstraete, K.
Funding Organization(s): Research Foundation - Flanders (FWO)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.192 (Depositor), 0.190 (DCC)
R-Value Work:
0.158 (Depositor), 0.160 (DCC)
R-Value Observed:
0.160 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Acetyl-CoA is produced by the citrate synthase homology module of ATP-citrate lyase.

Verstraete, K., Verschueren, K.H.G., Dansercoer, A., Savvides, S.N.

(2021) Nat Struct Mol Biol 28: 636-638

PubMed: 34294920 Search on PubMed
DOI: https://doi.org/10.1038/s41594-021-00624-3
Primary Citation of Related Structures:
6Z2H, 6ZNW

Organizational Affiliation

VIB-UGent Center for Inflammation Research, Ghent, Belgium. Kenneth.Verstraete@ugent.be.

Macromolecule Content

Total Structure Weight: 124.74 kDa
Atom Count: 9,165
Modelled Residue Count: 1,049
Deposited Residue Count: 1,080
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-citrate synthase	A, B, C, D	270	Homo sapiens	Mutation(s): 0 Gene Names: ACLY EC: 2.3.3.8
UniProt & NIH Common Fund Data Resources
Find proteins for P53396 (Homo sapiens) Explore P53396 Go to UniProtKB: P53396
PHAROS: P53396 GTEx: ENSG00000131473
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P53396
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Q5B (Subject of Investigation/LOI) Query on Q5B Download Ideal Coordinates CCD File SDF format, chain H [auth C] SDF format, chain E [auth A] SDF format, chain K [auth D] MOL2 format, chain H [auth C] MOL2 format, chain E [auth A] MOL2 format, chain K [auth D] mmCIF format, chain H [auth C] mmCIF format, chain E [auth A] mmCIF format, chain K [auth D]	E [auth A], H [auth C], K [auth D]	(3S)-citryl-Coenzyme A C₂₇ H₄₂ N₇ O₂₂ P₃ S IHVFHZGGMJDGGZ-VPXVXCNZSA-N		Interactions Focus chain E [auth A] Focus chain H [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth C] Focus chain K [auth D]
ACO (Subject of Investigation/LOI) Query on ACO Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth C] MOL2 format, chain G [auth A] MOL2 format, chain J [auth C] mmCIF format, chain G [auth A] mmCIF format, chain J [auth C]	G [auth A], J [auth C]	*ACETYL COENZYME A** C₂₃ H₃₈ N₇ O₁₇ P₃ S ZSLZBFCDCINBPY-ZSJPKINUSA-N		Interactions Focus chain G [auth A] Focus chain J [auth C] Interactions & Density Focus chain G [auth A] Focus chain J [auth C]
OAA (Subject of Investigation/LOI) Query on OAA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth C] MOL2 format, chain F [auth A] MOL2 format, chain I [auth C] mmCIF format, chain F [auth A] mmCIF format, chain I [auth C]	F [auth A], I [auth C]	OXALOACETATE ION C₄ H₃ O₅ KHPXUQMNIQBQEV-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain I [auth C] Interactions & Density Focus chain F [auth A] Focus chain I [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.192 (Depositor), 0.190 (DCC)
R-Value Work: 0.158 (Depositor), 0.160 (DCC)
R-Value Observed: 0.160 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.436	α = 90
b = 114.271	β = 90
c = 144.108	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2021-05-26

Deposition Author(s):

Verschueren, K.H.G.

Verstraete, K.

Funding Organization	Location	Grant Number
Research Foundation - Flanders (FWO)	Belgium	G0G0619N

Revision History (Full details and data files)

Version 1.0: 2021-05-26
Type: Initial release
Version 1.1: 2021-08-11
Changes: Database references
Version 1.2: 2021-08-25
Changes: Database references
Version 1.3: 2021-09-22
Changes: Data collection, Database references
Version 1.4: 2023-11-29
Changes: Data collection, Database references, Refinement description
Version 1.5: 2024-01-24
Changes: Refinement description

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Help and Resources

.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left:-5px; } 6Z2H | pdb_00006z2h

Citryl-CoA lyase module of human ATP citrate lyase in complex with (3S)-citryl-CoA.

Acetyl-CoA is produced by the citrate synthase homology module of ATP-citrate lyase.

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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