MolNFT v1 · #124687 · protein
Structure of cavab in complex with br-verapamil
5KMH · Ion transport protein: “Structure of cavab in complex with br-verapamil”. X-ray diffraction, 4 ligands (MC3, PX6, 6U8), 20 pockets (best druggability 0.79). MolNFT v1 #124687 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5KMH
- 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, PX6, 6U8, CA
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Ion transport protein | protein | 219 | 80% helix, 0% strand | A8EVM5 |
Ligands and binding sites
- MC3 · 1,2-dimyristoyl-rac-glycero-3-phosphocholine · ligand · 6 copies · chains A, C, B, D
- PX6 · 1,2-dipalmitoyl-sn-glycero-3-phosphate · ligand · 4 copies · chains A, B, D, C
- 6U8 · (2~{R})-2-(2-bromophenyl)-5-[2-(3,4-dimethoxyphenyl) ethyl-methyl-amino]-2-propan-2-yl-pentanenitrile · ligand · chains A, B, C, D
- CA · Calcium ion · metal · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 485 | 0.79 | 0.85 | 66 | CA, 6U8 |
| 2 | 252 | 0.61 | 0.80 | 32 | empty |
| 3 | 103 | 0.61 | 0.87 | 18 | empty |
| 4 | 78 | 0.58 | 0.87 | 15 | empty |
| 5 | 217 | 0.57 | 0.78 | 21 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1561 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1524 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1509 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 1454 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 22 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5KMH · Structure of CavAb in complex with Br-verapamil · 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 5KMH · PDBe 5KMH · UniProt A8EVM5
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