MolNFT v1 · #34959 · protein
Crystal structure of kcsa-Fab-tba complex in tl+
2DWD · Antibody Fab heavy chain: “Crystal structure of kcsa-Fab-tba complex in tl+”. X-ray diffraction, 4 ligands (F09, L2C, TBA), 4 pockets (best druggability 0.69). MolNFT v1 #34959 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2DWD
- Type
- protein
- Length
- 534 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody Fab heavy chain; Antibody Fab light chain; Voltage-gated potassium channel
- UniProt
- P0A334
- Ligands
- F09, L2C, TBA, TL
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antibody Fab heavy chain | protein | 219 | 4% helix, 49% strand | — |
| B | Antibody Fab light chain | protein | 212 | 6% helix, 53% strand | — |
| C | Voltage-gated potassium channel | protein | 103 | 75% helix, 0% strand | P0A334 |
Ligands and binding sites
- F09 · Nonan-1-ol · ligand · chains A, C
- L2C · (2S)-3-hydroxy-2-(nonanoyloxy)propyl laurate · ligand · chains C
- TBA · Tetrabutylammonium ion · ligand · chains C
- TL · Thallium (I) ion · metal · 4 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 756 | 0.69 | 0.76 | 56 | empty |
| 2 | 64 | 0.51 | 0.86 | 17 | empty |
| 3 | 125 | 0.47 | 0.79 | 28 | empty |
| 4 | 93 | 0.37 | 0.76 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1819 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 505 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 415 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2DWD · crystal structure of KcsA-FAB-TBA complex in Tl+ · 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 2DWD · PDBe 2DWD · UniProt P0A334
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