MolNFT v1 · #141275 · protein

The ternary structure of D-lactate dehydrogenase from fusobacterium nucleatum with NADH and oxamate

5Z21: “The ternary structure of D-lactate dehydrogenase from fusobacterium nucleatum with NADH and oxamate”. X-ray diffraction, 2 ligands (NAI, OXM), 13 pockets (best druggability 0.72). MolNFT v1 #141275 on GenesisL1: 3D structure…

PDB: 5Z21
Type: protein
Length: 1,319 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: D-lactate dehydrogenase
EC: 1.1.1.28
UniProt: Q8RG11
Ligands: NAI, OXM
Pockets: 13 · best druggability 0.72

Structure

x-ray diffraction · 3 distinct chains · 37% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	D-lactate dehydrogenase (EC 1.1.1.28)	protein	330	37% helix, 18% strand	Q8RG11
B, D	D-lactate dehydrogenase (EC 1.1.1.28)	protein	331	36% helix, 18% strand	Q8RG11
C	D-lactate dehydrogenase (EC 1.1.1.28)	protein	327	37% helix, 16% strand	Q8RG11

Ligands and binding sites

NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
OXM · Oxamic acid · ligand · 4 copies · chains A, B, C, D

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

Pockets

13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	723	0.72	0.79	97	empty
2	744	0.72	0.78	101	empty
3	332	0.72	0.84	45	NAI, OXM
4	76	0.72	0.96	16	empty
5	348	0.72	0.84	44	NAI, OXM

Interfaces

6 interfaces between chains.

C–D · 3008 Å² buried · 51 hydrogen bonds · protein-protein
A–B · 2996 Å² buried · 51 hydrogen bonds · protein-protein
A–C · 1121 Å² buried · 25 hydrogen bonds · protein-protein
B–D · 1116 Å² buried · 25 hydrogen bonds · protein-protein
A–D · 288 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5Z21 · The ternary structure of D-lactate dehydrogenase from Fusobacterium nucleatum with NADH… · 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 Q8RG11
Elsewhere: RCSB PDB 5Z21 · PDBe 5Z21 · UniProt Q8RG11

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