MolNFT v1 · #12914 · protein
Human phospholipase A2 complexed with a highly potent substrate anologue
1KVO: “Human phospholipase A2 complexed with a highly potent substrate anologue”. X-ray diffraction, 2 ligands (OAP, CA), 9 pockets (best druggability 0.78). MolNFT v1 #12914 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1KVO
- Type
- protein
- Length
- 744 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Human phospholipase A2
- EC
- 3.1.1.4
- UniProt
- P14555
- Ligands
- OAP, CA
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Human phospholipase A2 (EC 3.1.1.4) | protein | 124 | 48% helix, 7% strand | P14555 |
Ligands and binding sites
- OAP · 4-(S)-[(1-oxo-7-phenylheptyl)amino]-5-[4-(phenylmethyl)phenylthio]pentanoic acid · ligand · 6 copies · chains A, B, C, D, E, F
- CA · Calcium ion · metal · 12 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1029 | 0.78 | 0.80 | 97 | OAP |
| 2 | 746 | 0.75 | 0.80 | 78 | OAP |
| 3 | 517 | 0.73 | 0.81 | 60 | OAP |
| 4 | 338 | 0.67 | 0.81 | 36 | OAP |
| 5 | 332 | 0.66 | 0.81 | 40 | OAP |
Interfaces
12 interfaces between chains.
- C–D · 398 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 392 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 379 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 284 Ų buried · 1 hydrogen bond · protein-protein
- B–F · 271 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 disulfide (disulfide).
Compared structures
- 1KVO · Human phospholipase A2 complexed with a highly potent substrate anologue · the same entry in another collection · chain C against C, TM-score 1.00
- P14555 · AlphaFold monomer V2.0 prediction for phospholipase A2, membrane associated (P14555) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P14555
- Elsewhere: RCSB PDB 1KVO · PDBe 1KVO · UniProt P14555
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