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Crystal structure of rabbit ldha in complex with AP27460

Analyse Crystal structure of rabbit ldha in complex with AP27460 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4I8X
Type: protein
Length: 2,633 residues
Chains: 8
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
Ligands: 6P3
Pockets: 20 · best druggability 0.89

Structure

x-ray diffraction · 4 distinct chains · 45% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	L-lactate dehydrogenase a chain (EC 1.1.1.27)	protein	321	46% helix, 20% strand	P13491
B, C, D, E, H	L-lactate dehydrogenase a chain (EC 1.1.1.27)	protein	331	44% helix, 19% strand	P13491
F	L-lactate dehydrogenase a chain (EC 1.1.1.27)	protein	329	45% helix, 19% strand	P13491
G	L-lactate dehydrogenase a chain (EC 1.1.1.27)	protein	328	46% helix, 19% strand	P13491

Ligands and binding sites

6P3 · 6-phenylpyridine-3-carboxylic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H

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	1130	0.89	0.91	116	empty
2	1117	0.89	0.91	117	empty
3	895	0.82	0.84	89	6P3
4	64	0.69	0.96	14	empty
5	70	0.68	0.95	16	empty

Interfaces

14 interfaces between chains.

E–G · 2915 Å² buried · 25 hydrogen bonds · protein-protein
B–D · 2882 Å² buried · 25 hydrogen bonds · protein-protein
A–C · 2880 Å² buried · 24 hydrogen bonds · protein-protein
F–H · 2865 Å² buried · 25 hydrogen bonds · protein-protein
C–D · 1789 Å² buried · 32 hydrogen bonds · protein-protein

Compared structures

4I8X · Crystal structure of rabbit LDHA in complex with AP27460 · the same entry in another collection · chain H against H, TM-score 1.00
P13491 · AlphaFold monomer V2.0 prediction for L-lactate dehydrogenase a chain (P13491) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 4I8X · PDBe 4I8X · UniProt P13491

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