Research workbench
Crystal structure of anti-HIV-1 V3 Fab 3074 in complex with a UR29 V3 peptide
Analyse Crystal structure of anti-HIV-1 V3 Fab 3074 in complex with a UR29 V3 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MLY
- Type
- protein
- Length
- 912 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Human monoclonal anti-HIV-1 GP120 V3 antibody 3074 Fab light chain; Human monoclonal…
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, M | Human monoclonal anti-HIV-1 GP120 V3 antibody 3074 Fab light chain | protein | 214 | 7% helix, 50% strand | — |
| H, I | Human monoclonal anti-HIV-1 GP120 V3 antibody 3074 Fab heavy chain | protein | 230 | 7% helix, 53% strand | — |
| P, Q | HIV-1 GP120 third variable region (V3) crown | protein | 12 | 0% helix, 25% strand | — |
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 849 | 0.78 | 0.82 | 98 | empty |
| 2 | 1029 | 0.75 | 0.78 | 93 | empty |
| 3 | 233 | 0.57 | 0.79 | 37 | empty |
| 4 | 249 | 0.54 | 0.77 | 34 | empty |
| 5 | 90 | 0.46 | 0.80 | 25 | empty |
Interfaces
10 interfaces between chains.
- M–I · 1904 Ų buried · 16 hydrogen bonds · protein-protein
- L–H · 1808 Ų buried · 18 hydrogen bonds · protein-protein
- H–I · 812 Ų buried · 7 hydrogen bonds · protein-protein
- H–P · 638 Ų buried · 17 hydrogen bonds · protein-protein
- I–Q · 610 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 3MLY · Crystal structure of anti-HIV-1 V3 Fab 3074 in complex with a UR29 V3 peptide · 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 3MLY · PDBe 3MLY
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