Research workbench
Structure of a single domain camelid antibody fragment cab-G10S in complex with the blap beta-lactamase from bacillus licheniformis
Analyse Structure of a single domain camelid antibody fragment cab-G10S in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LWF
- Type
- protein
- Length
- 757 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-G10S
- EC
- 3.5.2.6
- UniProt
- P00808
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 259 | 43% helix, 18% strand | P00808 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 258 | 42% helix, 18% strand | P00808 |
| C | Camelid heavy-chain antibody variable fragment cab-G10S | protein | 122 | 5% helix, 46% strand | — |
| D | Camelid heavy-chain antibody variable fragment cab-G10S | protein | 118 | 5% helix, 42% strand | — |
Ligands and binding sites
- ACT · Acetate ion · additive · 5 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1050 | 0.75 | 0.78 | 81 | empty |
| 2 | 814 | 0.72 | 0.77 | 78 | empty |
| 3 | 59 | 0.47 | 0.85 | 17 | empty |
| 4 | 69 | 0.43 | 0.81 | 19 | empty |
| 5 | 66 | 0.32 | 0.75 | 19 | ACT |
Interfaces
5 interfaces between chains.
- B–D · 653 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 624 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 462 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 152 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 54 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5LWF · Structure of a single domain camelid antibody fragment cAb-G10S 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 5LWF · PDBe 5LWF · UniProt P00808
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