MolNFT v1 · #100574 · protein
Structure of a single-domain camelid antibody fragment cab-F11N in complex with the blap beta-lactamase from bacillus licheniformis
4N1H: “Structure of a single-domain camelid antibody fragment cab-F11N in complex with the blap beta-lactamase from…”. X-ray diffraction, 7 pockets (best druggability 0.56). MolNFT v1 #100574 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4N1H
- Type
- protein
- Length
- 767 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase; Camelid heavy-chain antibody variable fragment cab-F11N
- EC
- 3.5.2.6
- UniProt
- P00808
- Pockets
- 7 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 257 | 42% helix, 19% strand | P00808 |
| B, D | Camelid heavy-chain antibody variable fragment cab-F11N | protein | 126 | 7% helix, 44% strand | — |
| C | Beta-lactamase (EC 3.5.2.6) | protein | 258 | 42% helix, 18% strand | P00808 |
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 253 | 0.56 | 0.78 | 34 | empty |
| 2 | 103 | 0.46 | 0.79 | 19 | empty |
| 3 | 88 | 0.44 | 0.79 | 20 | empty |
| 4 | 123 | 0.41 | 0.76 | 20 | empty |
| 5 | 75 | 0.30 | 0.73 | 15 | empty |
Interfaces
3 interfaces between chains.
- C–D · 469 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 439 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 433 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4N1H · Structure of a single-domain camelid antibody fragment cAb-F11N in complex with the BlaP… · the same entry in another collection · chain A against A, TM-score 1.00
- P00808 · AlphaFold monomer V2.0 prediction for beta-lactamase (P00808) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P00808
- Elsewhere: RCSB PDB 4N1H · PDBe 4N1H · UniProt P00808
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