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Crystal structure of monoclinic rabbit muscle lactate dehydrogenase with four tetramers as the asymmetric unit

Analyse Crystal structure of monoclinic rabbit muscle lactate dehydrogenase with four… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6P6U
Type: protein
Length: 5,296 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
Ligands: AMP
Pockets: 20 · best druggability 0.89

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 20% strand (DSSP).

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

Ligands and binding sites

AMP · Adenosine monophosphate · ligand · 2 copies · chains C, E

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	1191	0.89	0.91	126	empty
2	1128	0.89	0.91	121	empty
3	773	0.89	0.92	110	empty
4	527	0.86	0.92	75	empty
5	303	0.82	0.93	45	empty

Interfaces

25 interfaces between chains.

B–C · 2905 Å² buried · 25 hydrogen bonds · protein-protein
M–P · 2897 Å² buried · 23 hydrogen bonds · protein-protein
E–H · 2895 Å² buried · 23 hydrogen bonds · protein-protein
I–L · 2880 Å² buried · 22 hydrogen bonds · protein-protein
J–K · 2877 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

6P6U · Crystal Structure of Monoclinic Rabbit Muscle Lactate Dehydrogenase with Four Tetramers… · 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 6P6U · PDBe 6P6U · UniProt P13491

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