MolNFT v1 · #117567 · protein
Kcsa with V76ESTER+G77DA mutations
5EC2 · Antibody Fab fragment light chain: “Kcsa with V76ESTER+G77DA mutations”. X-ray diffraction, 4 ligands (LHV, F09, DGA), 5 pockets (best druggability 0.67). MolNFT v1 #117567 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5EC2
- Type
- protein
- Length
- 532 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody Fab fragment light chain; PH-gated potassium channel kcsa
- UniProt
- P0A334
- Ligands
- LHV, F09, DGA, K
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antibody Fab fragment light chain | protein | 219 | 3% helix, 48% strand | — |
| B | Antibody Fab fragment light chain | protein | 212 | 7% helix, 50% strand | — |
| C | PH-gated potassium channel kcsa | protein | 101 | 76% helix, 0% strand | P0A334 |
Ligands and binding sites
- LHV · (2S)-2-hydroxy-3-methylbutanoic acid · ligand · chains C
- F09 · Nonan-1-ol · ligand · chains A, C
- DGA · Diacyl glycerol · ligand · chains C
- K · Potassium ion · metal · 6 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 752 | 0.67 | 0.75 | 62 | empty |
| 2 | 62 | 0.48 | 0.85 | 17 | empty |
| 3 | 61 | 0.48 | 0.84 | 17 | empty |
| 4 | 138 | 0.45 | 0.77 | 29 | empty |
| 5 | 97 | 0.37 | 0.75 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1853 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 478 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 433 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 covalent, 1 d-amino (disulfide, covalent ligand, D-amino acid).
Compared structures
- 5EC2 · KcsA with V76ester+G77dA mutations · the same entry in another collection · chain B against B, 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 5EC2 · PDBe 5EC2 · UniProt P0A334
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