2IZZ | pdb_00002izz

Crystal structure of human pyrroline-5-carboxylate reductase

PDB DOI: https://doi.org/10.2210/pdb2IZZ/pdb

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

Deposited: 2006-07-31 Released: 2006-08-01
Deposition Author(s): Pike, A.C.W., Guo, K., Kavanagh, K., Pilka, E.S., Berridge, G., Colebrook, S., Bray, J., Salah, E., Savitsky, P., Papagrigoriou, E., Turnbull, A.P., von Delft, F., Arrowsmith, C., Edwards, A., Weigelt, J., Sundstrom, M., Oppermann, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.190 (Depositor), 0.195 (DCC)
R-Value Work:
0.166 (Depositor), 0.170 (DCC)
R-Value Observed:
0.167 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of Human Pyrroline-5-Carboxylate Reductase

Pike, A.C.W., Guo, K., Kavanagh, K., Pilka, E.S., Berridge, G., Colebrook, S., Bray, J., Salah, E., Savitsky, P., Papagrigoriou, E., Turnbull, A.P., von Delft, F., Arrowsmith, C., Edwards, A., Weigelt, J., Sundstrom, M., Oppermann, U.

To be published.

Macromolecule Content

Total Structure Weight: 173.97 kDa
Atom Count: 10,933
Modeled Residue Count: 1,375
Deposited Residue Count: 1,610
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PYRROLINE-5-CARBOXYLATE REDUCTASE 1	A, B, C, D, E	322	Homo sapiens	Mutation(s): 0 EC: 1.5.1.2
UniProt & NIH Common Fund Data Resources
Find proteins for P32322 (Homo sapiens) Explore P32322 Go to UniProtKB: P32322
PHAROS: P32322 GTEx: ENSG00000183010
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P32322
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain N [auth D] SDF format, chain P [auth E] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D] MOL2 format, chain P [auth E] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth C] mmCIF format, chain N [auth D] mmCIF format, chain P [auth E]	F [auth A], J [auth B], K [auth C], N [auth D], P [auth E]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain N [auth D] Focus chain P [auth E] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain N [auth D] Focus chain P [auth E]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain Q [auth E] SDF format, chain O [auth D] SDF format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain Q [auth E] MOL2 format, chain O [auth D] MOL2 format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C] mmCIF format, chain Q [auth E] mmCIF format, chain O [auth D] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth A] L [auth C] M [auth C] G [auth A], H [auth A], I [auth A], L [auth C], M [auth C], O [auth D], Q [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.190 (Depositor), 0.195 (DCC)
R-Value Work: 0.166 (Depositor), 0.170 (DCC)
R-Value Observed: 0.167 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.453	α = 90
b = 177.944	β = 106.7
c = 87.916	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2006-08-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-08-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2018-01-24
Changes: Database references, Structure summary
Version 1.3: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description