1VM6 | pdb_00001vm6

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 (Depositor), 0.217 (DCC)
R-Value Work:
0.171 (Depositor), 0.176 (DCC)
R-Value Observed:
0.173 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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
Modeled Residue Count: 865
Deposited Residue Count: 912
Unique protein chains: 1

Macromolecules

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| 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 (PDB Primary Data), 1.17.1.8 (UniProt)
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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 Y [auth D] SDF format, chain T [auth C] SDF format, chain N [auth B] SDF format, chain G [auth A] MOL2 format, chain Y [auth D] MOL2 format, chain T [auth C] MOL2 format, chain N [auth B] MOL2 format, chain G [auth A] mmCIF format, chain Y [auth D] mmCIF format, chain T [auth C] mmCIF format, chain N [auth B] mmCIF format, chain G [auth A]	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 V [auth C] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] MOL2 format, chain V [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] mmCIF format, chain V [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B]	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] mmCIF 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 K [auth B] SDF format, chain X [auth D] SDF format, chain W [auth D] SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain X [auth D] MOL2 format, chain W [auth D] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain X [auth D] mmCIF format, chain W [auth D] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	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]