Research workbench
Crystal structure of rabbit ldha in complex with AP28161 and AP28122
Analyse Crystal structure of rabbit ldha in complex with AP28161 and AP28122 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4I9N
- Type
- protein
- Length
- 2,620 residues
- Chains
- 8
- 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
- 1E6, 1E5
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 6 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 324 | 45% helix, 19% strand | P13491 |
| C | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 328 | 45% helix, 18% strand | P13491 |
| D, E | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 331 | 46% helix, 19% strand | P13491 |
| F | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 329 | 45% helix, 19% strand | P13491 |
| G | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 328 | 45% helix, 19% strand | P13491 |
| H | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 325 | 45% helix, 19% strand | P13491 |
Ligands and binding sites
- 1E6 · 6-({2-[(5-chloro-4-{[(2S)-2,3-dihydroxypropyl]oxy}-2-methoxyphenyl)amino]-2-oxoethyl}sulfanyl)pyridine-3-carboxylic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- 1E5 · 6-[3-(carboxymethoxy)-5-fluorophenyl]pyridine-3-carboxylic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
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 | 1137 | 0.89 | 0.91 | 116 | empty |
| 2 | 868 | 0.88 | 0.91 | 95 | empty |
| 3 | 343 | 0.83 | 0.92 | 42 | empty |
| 4 | 944 | 0.83 | 0.84 | 89 | 1E5 |
| 5 | 70 | 0.71 | 0.96 | 14 | empty |
Interfaces
14 interfaces between chains.
- E–G · 2936 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 2890 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 2868 Ų buried · 25 hydrogen bonds · protein-protein
- F–H · 2867 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1791 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 4I9N · Crystal structure of rabbit LDHA in complex with AP28161 and AP28122 · the same entry in another collection · chain H against H, 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 H 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 4I9N · PDBe 4I9N · UniProt P13491
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