Research workbench
Rabbit muscle L-lactate dehydrogenase in complex with citrate
Analyse Rabbit muscle L-lactate dehydrogenase in complex with citrate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7P4G
- Type
- protein
- Length
- 5,221 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
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 7 distinct chains · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 320 | 46% helix, 20% strand | P13491 |
| B, F | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 322 | 46% helix, 19% strand | P13491 |
| C | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 327 | 43% helix, 20% strand | P13491 |
| D, G, L, M, N, O | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 331 | 45% helix, 19% strand | P13491 |
| H, K | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 330 | 46% helix, 22% strand | P13491 |
| J | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 319 | 45% helix, 22% strand | P13491 |
| P | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 325 | 46% helix, 19% strand | P13491 |
Ligands and binding sites
- CIT · Citric acid · additive · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
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 | 1115 | 0.89 | 0.91 | 117 | empty |
| 2 | 1121 | 0.89 | 0.91 | 119 | empty |
| 3 | 1108 | 0.89 | 0.91 | 120 | empty |
| 4 | 726 | 0.87 | 0.90 | 82 | empty |
| 5 | 356 | 0.83 | 0.92 | 47 | empty |
Interfaces
35 interfaces between chains.
- I–K · 2980 Ų buried · 27 hydrogen bonds · protein-protein
- J–L · 2975 Ų buried · 32 hydrogen bonds · protein-protein
- N–P · 2971 Ų buried · 27 hydrogen bonds · protein-protein
- F–H · 2961 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 2954 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 7P4G · Rabbit Muscle L-lactate dehydrogenase in complex with citrate · 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 7P4G · PDBe 7P4G · UniProt P13491
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