2J40 | pdb_00002j40

1-pyrroline-5-carboxylate dehydrogenase from Thermus thermophilus with bound inhibitor L-proline and NAD.

PDB DOI: https://doi.org/10.2210/pdb2J40/pdb

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

Deposited: 2006-08-24 Released: 2007-10-02
Deposition Author(s): Inagaki, E., Sakamoto, K., Nishio, M., Yokoyama, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.189 (Depositor)
R-Value Work:
0.140 (Depositor), 0.143 (DCC)
R-Value Observed:
0.142 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 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: 116.81 kDa
Atom Count: 9,053
Modeled Residue Count: 1,032
Deposited Residue Count: 1,032
Unique protein chains: 1

Macromolecules

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| 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 (PDB Primary Data), 1.2.1.88 (UniProt)
UniProt
Find proteins for Q5SI02 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SI02 Go to UniProtKB: Q5SI02
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 K [auth B] SDF format, chain D [auth A] MOL2 format, chain K [auth B] MOL2 format, chain D [auth A] mmCIF format, chain K [auth B] mmCIF format, chain D [auth A]	D [auth A], K [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain D [auth A] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain K [auth B]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain J [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] mmCIF format, chain J [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B]	J [auth B], N [auth B], O [auth B], P [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain J [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain J [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]
MRD Query on MRD Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain Q [auth B] MOL2 format, chain G [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain G [auth A] mmCIF format, chain Q [auth B]	G [auth A], Q [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] Interactions & Density Focus chain G [auth A] Focus chain Q [auth B]
PRO Query on PRO Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain I [auth B]	C [auth A], I [auth B]	PROLINE C₅ H₉ N O₂ ONIBWKKTOPOVIA-BYPYZUCNSA-N		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain F [auth A]	E [auth A], F [auth A], L [auth B], M [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain R [auth B] MOL2 format, chain H [auth A] MOL2 format, chain R [auth B] mmCIF format, chain H [auth A] mmCIF format, chain R [auth B]	H [auth A], R [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain R [auth B] Interactions & Density Focus chain H [auth A] Focus chain R [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO Query on CSO	A, B	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.189 (Depositor)
R-Value Work: 0.140 (Depositor), 0.143 (DCC)
R-Value Observed: 0.142 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.043	α = 90
b = 102.043	β = 90
c = 278.6	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2007-10-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-10-02
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: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description
Version 1.4: 2024-10-16
Changes: Structure summary