2J5N

1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE FROM THERMUS THERMOPHIRUS WITH BOUND INHIBITOR GLYCINE AND NAD.

PDB DOI: https://doi.org/10.2210/pdb2J5N/pdb

Classification: OXIDOREDUCTASE
Organism(s): Thermus thermophilus HB8
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2006-09-19 Released: 2007-10-16
Deposition Author(s): Inagaki, E., Sakamoto, K., Nishio, M., Yokoyama, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.63 Å
R-Value Free: 0.174
R-Value Work: 0.146
R-Value Observed: 0.147

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 Ternary Complex of Delta1-Pyrroline-5-Carboxylate Dehydrogenase with Substrate Mimic and Co-Factoer

Inagaki, E., Sakamoto, K., Nishio, M., Yokoyama, S., Tahirov, T.H.

To be published.

Macromolecule Content

Total Structure Weight: 117.05 kDa
Atom Count: 9,469
Modelled Residue Count: 1,032
Deposited Residue Count: 1,032
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE	A, B	516	Thermus thermophilus HB8	Mutation(s): 0 EC: 1.5.1.12
UniProt
Find proteins for Q5SI02 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SI02 Go to UniProtKB: Q5SI02
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5SI02
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain M [auth B] MOL2 format, chain D [auth A] MOL2 format, chain M [auth B]	D [auth A], M [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain D [auth A] Focus chain M [auth B] Interactions & Density Focus chain D [auth A] Focus chain M [auth B]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain P [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain P [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B]	H [auth A] I [auth A] J [auth A] P [auth B] S [auth B] H [auth A], I [auth A], J [auth A], P [auth B], S [auth B], T [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain P [auth B] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain P [auth B] Focus chain S [auth B] Focus chain T [auth B]
MRD Query on MRD Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] MOL2 format, chain G [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B]	G [auth A], Q [auth B], R [auth B]	(4R)-2-METHYLPENTANE-2,4-DIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-RXMQYKEDSA-N		Interactions Focus chain G [auth A] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain G [auth A] Focus chain Q [auth B] Focus chain R [auth B]
GLY Query on GLY Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain L [auth B] MOL2 format, chain C [auth A] MOL2 format, chain L [auth B]	C [auth A], L [auth B]	GLYCINE C₂ H₅ N O₂ DHMQDGOQFOQNFH-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain L [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B]	E [auth A], F [auth A], N [auth B], O [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain N [auth B] Focus chain O [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain U [auth B] MOL2 format, chain K [auth A] MOL2 format, chain U [auth B]	K [auth A], U [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain U [auth B] Interactions & Density Focus chain K [auth A] Focus chain U [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.63 Å
R-Value Free: 0.174
R-Value Work: 0.146
R-Value Observed: 0.147
Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.589	α = 90
b = 102.589	β = 90
c = 278.637	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
REFMAC	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-10-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-10-16
Type: Initial release
Version 1.1: 2012-08-29
Changes: Data collection, Database references, Derived calculations, Other, Structure summary, Version format compliance
Version 1.2: 2019-08-21
Changes: Data collection, Database references
Version 1.3: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description