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Crystal structure of human Fab CAP256-VRC26.04, a potent V1V2-directed HIV-1 neutralizing antibody
Analyse Crystal structure of human Fab CAP256-VRC26.04, a potent V1V2-directed HIV-1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ORG
- Type
- protein
- Length
- 1,778 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CAP256-VRC26.04 light chain; CAP256-VRC26.04 heavy chain
- Pockets
- 19 · best druggability 0.74
Structure
x-ray diffraction · 8 distinct chains · 6% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | CAP256-VRC26.04 light chain | protein | 211 | 4% helix, 41% strand | — |
| H | CAP256-VRC26.04 heavy chain | protein | 238 | 6% helix, 46% strand | — |
| B | CAP256-VRC26.04 light chain | protein | 208 | 5% helix, 44% strand | — |
| A | CAP256-VRC26.04 heavy chain | protein | 232 | 5% helix, 50% strand | — |
| D | CAP256-VRC26.04 light chain | protein | 208 | 8% helix, 45% strand | — |
| C | CAP256-VRC26.04 heavy chain | protein | 237 | 5% helix, 44% strand | — |
| F | CAP256-VRC26.04 light chain | protein | 209 | 8% helix, 44% strand | — |
| E | CAP256-VRC26.04 heavy chain | protein | 235 | 5% helix, 49% strand | — |
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 780 | 0.74 | 0.79 | 98 | empty |
| 2 | 711 | 0.72 | 0.79 | 94 | empty |
| 3 | 942 | 0.72 | 0.76 | 84 | empty |
| 4 | 690 | 0.70 | 0.78 | 62 | empty |
| 5 | 804 | 0.70 | 0.76 | 76 | empty |
Interfaces
13 interfaces between chains.
- B–A · 1769 Ų buried · 11 hydrogen bonds · protein-protein
- D–C · 1726 Ų buried · 14 hydrogen bonds · protein-protein
- F–E · 1723 Ų buried · 9 hydrogen bonds · protein-protein
- L–H · 1654 Ų buried · 12 hydrogen bonds · protein-protein
- H–E · 709 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 5 modified (disulfide, sulfation).
Compared structures
- 4ORG · Crystal structure of human Fab CAP256-VRC26.04, a potent V1V2-directed HIV-1 neutralizing… · 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 4ORG · PDBe 4ORG
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