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Crystal structure of D-isomer specific 2-hydroxyacid dehydrogenase from lactobacillus delbrueckii ssp. bulgaricus: NAD complexed form

Analyse Crystal structure of D-isomer specific 2-hydroxyacid dehydrogenase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2YQ5
Type: protein
Length: 1,308 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: D-isomer specific 2-hydroxyacid dehydrogenase
UniProt: Q1GAA2
Ligands: NAD
Pockets: 14 · best druggability 0.72

Structure

x-ray diffraction · 4 distinct chains · 41% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	D-isomer specific 2-hydroxyacid dehydrogenase	protein	328	40% helix, 16% strand	Q1GAA2
B	D-isomer specific 2-hydroxyacid dehydrogenase	protein	328	40% helix, 16% strand	Q1GAA2
C	D-isomer specific 2-hydroxyacid dehydrogenase	protein	331	42% helix, 16% strand	Q1GAA2
D	D-isomer specific 2-hydroxyacid dehydrogenase	protein	321	40% helix, 16% strand	Q1GAA2

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	811	0.72	0.77	66	NAD
2	733	0.70	0.77	64	NAD
3	624	0.70	0.78	67	empty
4	518	0.69	0.79	70	empty
5	712	0.68	0.76	62	NAD

Interfaces

6 interfaces between chains.

A–B · 2830 Å² buried · 36 hydrogen bonds · protein-protein
C–D · 2825 Å² buried · 37 hydrogen bonds · protein-protein
A–D · 605 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 580 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 224 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

2YQ5 · Crystal Structure of D-isomer specific 2-hydroxyacid dehydrogenase from Lactobacillus… · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q1GAA2
Elsewhere: RCSB PDB 2YQ5 · PDBe 2YQ5 · UniProt Q1GAA2

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