2H5G | pdb_00002h5g

Crystal structure of human pyrroline-5-carboxylate synthetase

PDB DOI: https://doi.org/10.2210/pdb2H5G/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2006-05-26 Released: 2006-06-23
Deposition Author(s): Papagrigoriou, E., Shafqat, N., Turnbull, A.P., Berridge, G., Hozjan, V., Kavanagh, K., Gileadi, O., Smee, C., Bray, J., Gorrec, F., Sundstrom, M., Arrowsmith, C., Weigelt, J., Edwards, A., Oppermann, U., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.272 (Depositor), 0.299 (DCC)
R-Value Work:
0.230 (Depositor), 0.262 (DCC)
R-Value Observed:
0.232 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of human pyrroline-5-carboxylate synthetase

Papagrigoriou, E., Shafqat, N., Turnbull, A.P., Berridge, G., Hozjan, V., Kavanagh, K., Gileadi, O., Smee, C., Bray, J., Gorrec, F., Sundstrom, M., Arrowsmith, C., Weigelt, J., Edwards, A., Oppermann, U.

To be published.

Macromolecule Content

Total Structure Weight: 104.05 kDa
Atom Count: 6,695
Modeled Residue Count: 842
Deposited Residue Count: 926
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Delta 1-pyrroline-5-carboxylate synthetase	A, B	463	Homo sapiens	Mutation(s): 6 Gene Names: ALDH18A1 EC: 1.2.1.41 (PDB Primary Data), 2.7.2.11 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P54886 (Homo sapiens) Explore P54886 Go to UniProtKB: P54886
PHAROS: P54886 GTEx: ENSG00000059573
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P54886
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth B] G [auth B] C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], H [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.272 (Depositor), 0.299 (DCC)
R-Value Work: 0.230 (Depositor), 0.262 (DCC)
R-Value Observed: 0.232 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.022	α = 90
b = 137.402	β = 90
c = 72.057	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2006-06-23

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2006-06-23
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary