2CNV | pdb_00002cnv

SAICAR-synthase from Saccharomyces cerevisiae complexed SAICAR

PDB DOI: https://doi.org/10.2210/pdb2CNV/pdb

Classification: LIGASE
Organism(s): Saccharomyces cerevisiae
Mutation(s): No

Deposited: 2006-05-24 Released: 2006-06-08
Deposition Author(s): Urusova, D.V., Antonyuk, S.V., Grebenko, A.I., Levdikov, V.M., Barynin, V.V., Popov, A.N., Lamzin, V.S., Melik-Adamyan, V.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.238 (Depositor), 0.238 (DCC)
R-Value Work:
0.173 (Depositor), 0.174 (DCC)
R-Value Observed:
0.177 (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

X-Ray Diffraction Study of the Complex of the Enzyme Saicar Synthase with the Reaction Product

Urusova, D.V., Levdikov, V.M., Antonyuk, S.V., Grebenko, A.I., Lamzin, V.S., Melik-Adamyan, V.R.

(2006) Crystallogr Rep 51: 824

DOI: https://doi.org/10.1134/S1063774506050129

Macromolecule Content

Total Structure Weight: 35.46 kDa
Atom Count: 2,914
Modeled Residue Count: 300
Deposited Residue Count: 306
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHORIBOSYLAMINOIMIDAZOLE-SUCCINOCARBOXAMIDE SYNTHASE	A	306	Saccharomyces cerevisiae	Mutation(s): 0 EC: 6.3.2.6
UniProt
Find proteins for P27616 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P27616 Go to UniProtKB: P27616
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P27616
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SSS Query on SSS Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	N-{[5-AMINO-1-(5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-1H-IMIDAZOL-4-YL]CARBONYL}-L-ASPARTIC ACID C₁₃ H₁₉ N₄ O₁₂ P NAQGHJTUZRHGAC-PSYSQGJASA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
ASP Query on ASP Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	ASPARTIC ACID C₄ H₇ N O₄ CKLJMWTZIZZHCS-REOHCLBHSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.238 (Depositor), 0.238 (DCC)
R-Value Work: 0.173 (Depositor), 0.174 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.85	α = 90
b = 62.75	β = 90
c = 77.7	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2006-06-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-06-08
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations
Version 1.4: 2023-12-13
Changes: Data collection, Database references, Other, Refinement description
Version 1.5: 2024-11-20
Changes: Structure summary