MolNFT v1 · #124615 · protein
L-lactate dehydrogenase from rabbit muscle with the inhibitor 6DHNAD
5KKC · L-lactate dehydrogenase a chain: “L-lactate dehydrogenase from rabbit muscle with the inhibitor 6DHNAD”. X-ray diffraction, 2 ligands (6V0, SO4), 20 pockets (best druggability 0.89). MolNFT v1 #124615 on GenesisL1: 3D structure…
- PDB
- 5KKC
- Type
- protein
- Length
- 1,303 residues
- Chains
- 4
- 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
- 6V0, SO4
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 328 | 45% helix, 19% strand | P13491 |
| B | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 320 | 45% helix, 19% strand | P13491 |
| C | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 326 | 45% helix, 22% strand | P13491 |
| D | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 329 | 45% helix, 19% strand | P13491 |
Ligands and binding sites
- 6V0 · [[(2~{R},3~{S},4~{R},5~{R})-5-(5-aminocarbonyl-2~{H}-pyridin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 5 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1097 | 0.89 | 0.91 | 117 | SO4 |
| 2 | 251 | 0.73 | 0.87 | 40 | 6V0 |
| 3 | 190 | 0.70 | 0.88 | 31 | 6V0 |
| 4 | 65 | 0.69 | 0.96 | 16 | empty |
| 5 | 340 | 0.68 | 0.82 | 49 | 6V0 |
Interfaces
6 interfaces between chains.
- B–D · 2897 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 2862 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1743 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1665 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 983 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5KKC · l-lactate dehydrogenase from rabbit muscle with the inhibitor 6DHNAD · the same entry in another collection · chain B against B, 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 B 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 5KKC · PDBe 5KKC · UniProt P13491
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