MolNFT v1 · #184842 · protein

Rabbit muscle L-lactate dehydrogenase in complex with citrate

7P4G · L-lactate dehydrogenase a chain: “Rabbit muscle L-lactate dehydrogenase in complex with citrate”. X-ray diffraction, 20 pockets (best druggability 0.89). MolNFT v1 #184842 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 7P4G
Type: protein
Length: 5,221 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: L-lactate dehydrogenase a chain
EC: 1.1.1.27
UniProt: P13491
Pockets: 20 · best druggability 0.89

Structure

x-ray diffraction · 7 distinct chains · 45% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E, I	L-lactate dehydrogenase a chain (EC 1.1.1.27)	protein	320	46% helix, 20% strand	P13491
B, F	L-lactate dehydrogenase a chain (EC 1.1.1.27)	protein	322	46% helix, 19% strand	P13491
C	L-lactate dehydrogenase a chain (EC 1.1.1.27)	protein	327	43% helix, 20% strand	P13491
D, G, L, M, N, O	L-lactate dehydrogenase a chain (EC 1.1.1.27)	protein	331	45% helix, 19% strand	P13491
H, K	L-lactate dehydrogenase a chain (EC 1.1.1.27)	protein	330	46% helix, 22% strand	P13491
J	L-lactate dehydrogenase a chain (EC 1.1.1.27)	protein	319	45% helix, 22% strand	P13491
P	L-lactate dehydrogenase a chain (EC 1.1.1.27)	protein	325	46% helix, 19% strand	P13491

Ligands and binding sites

CIT · Citric acid · additive · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1115	0.89	0.91	117	empty
2	1121	0.89	0.91	119	empty
3	1108	0.89	0.91	120	empty
4	726	0.87	0.90	82	empty
5	356	0.83	0.92	47	empty

Interfaces

35 interfaces between chains.

I–K · 2980 Å² buried · 27 hydrogen bonds · protein-protein
J–L · 2975 Å² buried · 32 hydrogen bonds · protein-protein
N–P · 2971 Å² buried · 27 hydrogen bonds · protein-protein
F–H · 2961 Å² buried · 28 hydrogen bonds · protein-protein
B–D · 2954 Å² buried · 30 hydrogen bonds · protein-protein

Compared structures

7P4G · Rabbit Muscle L-lactate dehydrogenase in complex with citrate · the same entry in another collection · chain P against P, 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 P13491
Elsewhere: RCSB PDB 7P4G · PDBe 7P4G · UniProt P13491

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