2CNU

Atomic resolution structure of SAICAR-synthase from Saccharomyces cerevisiae complexed with aspartic acid

PDB DOI: https://doi.org/10.2210/pdb2CNU/pdb

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

Deposited: 2006-05-24 Released: 2006-06-07
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, W.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.05 Å
R-Value Free:
0.159 (Depositor), 0.170 (DCC)
R-Value Work:
0.132 (Depositor), 0.150 (DCC)
R-Value Observed:
0.134 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Saicar Synthase: Substrate Recognition, Conformational Flexibility and Catalysis.

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

To be published.

Macromolecule Content

Total Structure Weight: 35.62 kDa
Atom Count: 3,573
Modelled Residue Count: 303
Deposited Residue Count: 306
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P27616
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ASP Query on ASP Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	B [auth A], C [auth A], D [auth A]	ASPARTIC ACID C₄ H₇ N O₄ CKLJMWTZIZZHCS-REOHCLBHSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.05 Å
R-Value Free: 0.159 (Depositor), 0.170 (DCC)
R-Value Work: 0.132 (Depositor), 0.150 (DCC)
R-Value Observed: 0.134 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.023	α = 90
b = 62.497	β = 90
c = 78.273	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2006-06-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-06-07
Type: Initial release
Version 1.1: 2013-09-04
Changes: Atomic model, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
Version 1.2: 2019-07-24
Changes: Data collection, Derived calculations
Version 1.3: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description
Version 1.4: 2024-11-06
Changes: Structure summary