MolNFT v1 · #137297 · protein
Open conformation of kcsa non-inactivating E71A mutant
5VK6 · Antibody heavy chain: “Open conformation of kcsa non-inactivating E71A mutant”. X-ray diffraction, 3 ligands (F09, 1EM, K), 6 pockets (best druggability 0.68). MolNFT v1 #137297 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5VK6
- Type
- protein
- Length
- 527 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody heavy chain; Antibody light chain; PH-gated potassium channel kcsa
- UniProt
- P0A334
- Ligands
- F09, 1EM, K
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antibody heavy chain | protein | 219 | 4% helix, 49% strand | — |
| B | Antibody light chain | protein | 212 | 5% helix, 52% strand | — |
| C | PH-gated potassium channel kcsa | protein | 96 | 75% helix, 0% strand | P0A334 |
Ligands and binding sites
- F09 · Nonan-1-ol · ligand · chains A, C
- 1EM · (1S)-2-hydroxy-1-[(nonanoyloxy)methyl]ethyl myristate · ligand · chains C
- K · Potassium ion · metal · 7 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 767 | 0.68 | 0.76 | 60 | empty |
| 2 | 52 | 0.50 | 0.86 | 15 | empty |
| 3 | 62 | 0.48 | 0.85 | 16 | empty |
| 4 | 51 | 0.48 | 0.86 | 20 | empty |
| 5 | 171 | 0.46 | 0.75 | 29 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1820 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 480 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 437 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5VK6 · Open conformation of KcsA non-inactivating E71A mutant · 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 P0A334
- Elsewhere: RCSB PDB 5VK6 · PDBe 5VK6 · UniProt P0A334
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