Research workbench
Crystal structure of 3BNC60 Fab with P61A mutation
Analyse Crystal structure of 3BNC60 Fab with P61A mutation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GW4
- Type
- protein
- Length
- 822 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3BNC60 Fab light-chain; 3BNC60 Fab heavy-chain
- Ligands
- NAG
- Pockets
- 2 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | 3BNC60 Fab light-chain | protein | 198 | 7% helix, 52% strand | — |
| H | 3BNC60 Fab heavy-chain | protein | 213 | 8% helix, 51% strand | — |
| A | 3BNC60 Fab heavy-chain | protein | 212 | 8% helix, 51% strand | — |
| B | 3BNC60 Fab light-chain | protein | 199 | 7% helix, 53% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains L, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1110 | 0.81 | 0.82 | 156 | empty |
| 2 | 143 | 0.54 | 0.81 | 34 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1682 Ų buried · 16 hydrogen bonds · protein-protein
- L–H · 1634 Ų buried · 18 hydrogen bonds · protein-protein
- H–B · 192 Ų buried · 2 hydrogen bonds · protein-protein
- L–A · 177 Ų buried · 2 hydrogen bonds · protein-protein
- L–B · 129 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan, 1 modified (disulfide, N-glycosylation, cyclization).
Compared structures
- 4GW4 · Crystal structure of 3BNC60 Fab with P61A mutation · the same entry in another collection · chain L against L, 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
- Elsewhere: RCSB PDB 4GW4 · PDBe 4GW4
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