MolNFT v1 · #159970 · protein
Crystal structure of monoclinic rabbit muscle lactate dehydrogenase with four tetramers as the asymmetric unit
6P6U · L-lactate dehydrogenase a chain: “Crystal structure of monoclinic rabbit muscle lactate dehydrogenase with four tetramers as the asymmetric unit”. X-ray diffraction, 1 ligand (AMP), 20 pockets (best druggability 0.89). MolNFT v1…
- 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.
| Volume (ų) | 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 Ų buried · 25 hydrogen bonds · protein-protein
- M–P · 2897 Ų buried · 23 hydrogen bonds · protein-protein
- E–H · 2895 Ų buried · 23 hydrogen bonds · protein-protein
- I–L · 2880 Ų buried · 22 hydrogen bonds · protein-protein
- J–K · 2877 Ų 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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