Research workbench
Ldha structure in complex with inhibitor 14
Analyse Ldha structure in complex with inhibitor 14 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MVA
- Type
- protein
- Length
- 1,300 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
- P00338
- Ligands
- NAI, D4S, SO4
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 19% 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 | P00338 |
| B, C | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 325 | 46% helix, 19% strand | P00338 |
| D | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 322 | 46% helix, 19% strand | P00338 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- D4S · (6R)-6-(3-aminophenyl)-3-[(2-chlorophenyl)sulfanyl]-4-hydroxy-6-(thiophen-3-yl)-5,6-dihydro-2H-pyran-2-one · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains A, C, B, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 3 copies · chains A, 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1067 | 0.89 | 0.91 | 115 | SO4 |
| 2 | 82 | 0.71 | 0.95 | 18 | empty |
| 3 | 72 | 0.67 | 0.94 | 16 | empty |
| 4 | 470 | 0.65 | 0.77 | 43 | NAI, D4S |
| 5 | 438 | 0.65 | 0.78 | 48 | NAI, D4S |
Interfaces
6 interfaces between chains.
- C–D · 2919 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 2907 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 1674 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 1621 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 968 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6MVA · LDHA structure in complex with inhibitor 14 · the same entry in another collection · chain A against A, 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 P00338
- Elsewhere: RCSB PDB 6MVA · PDBe 6MVA · UniProt P00338
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