Research workbench
Crystal structure of rabbit anti-HIV-1 GP120 V2 Fab 16C2 in complex with V2 peptide conb
Analyse Crystal structure of rabbit anti-HIV-1 GP120 V2 Fab 16C2 in complex with V2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CEZ
- Type
- protein
- Length
- 448 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light chain of Fab fragment of rabbit anti-HIV1 GP120 V2 mab 16C2; Heavy chain of Fab…
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Light chain of Fab fragment of rabbit anti-HIV1 GP120 V2 mab 16C2 | protein | 212 | 8% helix, 53% strand | — |
| H | Heavy chain of Fab fragment of rabbit anti-HIV1 GP120 V2 mab 16C2 | protein | 222 | 5% helix, 45% strand | — |
| P | HIV-1 GP120 V2 peptide con B | protein | 14 | 71% helix, 0% strand | — |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 464 | 0.59 | 0.74 | 50 | empty |
| 2 | 86 | 0.37 | 0.76 | 17 | empty |
| 3 | 72 | 0.35 | 0.77 | 16 | empty |
| 4 | 56 | 0.28 | 0.74 | 16 | empty |
| 5 | 56 | 0.26 | 0.73 | 12 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1856 Ų buried · 14 hydrogen bonds · protein-protein
- H–P · 392 Ų buried · 4 hydrogen bonds · protein-protein
- L–P · 354 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 6CEZ · Crystal Structure of Rabbit Anti-HIV-1 gp120 V2 Fab 16C2 in complex with V2 peptide ConB · 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 6CEZ · PDBe 6CEZ
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