Research workbench
Structure of CavAb in complex with Diltiazem and Amlodipine
Analyse Structure of CavAb in complex with Diltiazem and Amlodipine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KE5
- Type
- protein
- Length
- 902 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.803
- Source
- Arcobacter butzleri RM4018
- Molecule
- Ion transport protein
- UniProt
- A8EVM5
- Ligands
- G3P, LPC, 6UB, D6C, CA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · resolution 2.803 · 2 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Ion transport protein | protein | 219 | 71% helix, 0% strand | A8EVM5 |
| B, D | Ion transport protein | protein | 232 | 74% helix, 0% strand | A8EVM5 |
Ligands and binding sites
- G3P · Sn-glycerol-3-phosphate · ligand · 5 copies · chains A, C, B, D
- LPC · [1-myristoyl-glycerol-3-yl]phosphonylcholine · ligand · 3 copies · chains A, B, C, D
- 6UB · amlodipine · ligand · chains B, D
- D6C · [(2~{S},3~{R})-5-[2-(dimethylamino)ethyl]-2-(4-methoxyphenyl)-4-oxidanylidene-2,3-dihydro-1,5-benzothiazepin-3-yl] ethanoate · ligand · chains A, 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 784 | 0.84 | 0.86 | 89 | CA, D6C |
| 2 | 215 | 0.62 | 0.81 | 21 | empty |
| 3 | 130 | 0.58 | 0.83 | 22 | empty |
| 4 | 85 | 0.57 | 0.86 | 19 | empty |
| 5 | 140 | 0.55 | 0.81 | 27 | empty |
Interfaces
5 interfaces between chains.
- B–D · 1681 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1634 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1526 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 1477 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 29 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6KE5 · Structure of cavab in complex with diltiazem and amlodipine · 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 6KE5 · PDBe 6KE5 · UniProt A8EVM5
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