MolNFT v1 · #124685 · protein
Structure of cavab in complex with nimodipine
5KMF · Ion transport protein: “Structure of cavab in complex with nimodipine”. X-ray diffraction, 3 ligands (MC3, 6U9, CA), 19 pockets (best druggability 0.85). MolNFT v1 #124685 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5KMF
- Type
- protein
- Length
- 876 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ion transport protein
- UniProt
- A8EVM5
- Ligands
- MC3, 6U9, CA
- Pockets
- 19 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Ion transport protein | protein | 219 | 79% helix, 0% strand | A8EVM5 |
Ligands and binding sites
- MC3 · 1,2-dimyristoyl-rac-glycero-3-phosphocholine · ligand · 14 copies · chains A, B, C, D
- 6U9 · nimodipine · ligand · chains A, C
- CA · Calcium ion · metal · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 931 | 0.85 | 0.86 | 105 | MC3, CA |
| 2 | 419 | 0.63 | 0.76 | 35 | empty |
| 3 | 179 | 0.55 | 0.79 | 17 | empty |
| 4 | 134 | 0.55 | 0.81 | 16 | empty |
| 5 | 161 | 0.55 | 0.79 | 20 | empty |
Interfaces
5 interfaces between chains.
- B–D · 1576 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1570 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1568 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1508 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 18 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5KMF · Structure of CavAb in complex with nimodipine · 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 A8EVM5
- Elsewhere: RCSB PDB 5KMF · PDBe 5KMF · UniProt A8EVM5
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