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Structure of the unliganded Fab from HIV-1 neutralising antibody CAP248-2B that binds to the GP120 C-terminus - GP41 interface
Analyse Structure of the unliganded Fab from HIV-1 neutralising antibody CAP248-2B that… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5F89
- Type
- protein
- Length
- 899 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CAP248-2B heavy chain; CAP248-2B light chain
- Pockets
- 9 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, A | CAP248-2B heavy chain | protein | 228 | 4% helix, 50% strand | — |
| L | CAP248-2B light chain | protein | 221 | 6% helix, 52% strand | — |
| B | CAP248-2B light chain | protein | 222 | 5% helix, 54% strand | — |
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 522 | 0.60 | 0.74 | 56 | empty |
| 2 | 568 | 0.60 | 0.74 | 60 | empty |
| 3 | 167 | 0.56 | 0.81 | 29 | empty |
| 4 | 118 | 0.44 | 0.77 | 28 | empty |
| 5 | 119 | 0.44 | 0.78 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2148 Ų buried · 24 hydrogen bonds · protein-protein
- H–L · 2047 Ų buried · 23 hydrogen bonds · protein-protein
- H–B · 378 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 modified (disulfide, cyclization).
Compared structures
- 5F89 · Structure of the Unliganded Fab from HIV-1 Neutralising Antibody CAP248-2B that Binds to… · the same entry in another collection · chain H against H, 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 5F89 · PDBe 5F89
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