1VM6

Crystal structure of Dihydrodipicolinate reductase (TM1520) from Thermotoga maritima at 2.27 A resolution

PDB DOI: https://doi.org/10.2210/pdb1VM6/pdb

Classification: OXIDOREDUCTASE
Organism(s): Thermotoga maritima
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2004-09-03 Released: 2004-09-21
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free: 0.213
R-Value Work: 0.171
R-Value Observed: 0.173

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of Dihydrodipicolinate reductase (TM1520) from Thermotoga maritima at 2.27 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 105.1 kDa
Atom Count: 7,538
Modelled Residue Count: 865
Deposited Residue Count: 912
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrodipicolinate reductase	A, B, C, D	228	Thermotoga maritima	Mutation(s): 0 Gene Names: dapB, TM1520 EC: 1.3.1.26
UniProt
Find proteins for Q9X1K8 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X1K8 Go to UniProtKB: Q9X1K8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9X1K8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain N [auth B] SDF format, chain T [auth C] SDF format, chain Y [auth D] MOL2 format, chain G [auth A] MOL2 format, chain N [auth B] MOL2 format, chain T [auth C] MOL2 format, chain Y [auth D]	G [auth A], N [auth B], T [auth C], Y [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain G [auth A] Focus chain N [auth B] Focus chain T [auth C] Focus chain Y [auth D] Interactions & Density Focus chain G [auth A] Focus chain N [auth B] Focus chain T [auth C] Focus chain Y [auth D]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain V [auth C] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain V [auth C]	O [auth B], P [auth B], Q [auth B], V [auth C]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain V [auth C] Interactions & Density Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain V [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain U [auth C] MOL2 format, chain U [auth C]	U [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain U [auth C] Interactions & Density Focus chain U [auth C]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D]	E [auth A] F [auth A] H [auth B] I [auth B] J [auth B] E [auth A], F [auth A], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B], R [auth C], S [auth C], W [auth D], X [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain W [auth D] Focus chain X [auth D]