MolNFT v1 · #71693 · protein
Crystal structure of anti-HIV-1 V3 Fab 2557 in complex with a NY5 V3 peptide
3MLR · Human monoclonal anti-HIV-1 GP120 V3 antibody 2557 Fab…: “Crystal structure of anti-HIV-1 V3 Fab 2557 in complex with a NY5 V3 peptide”. X-ray diffraction, 5 pockets (best druggability 0.52). MolNFT v1 #71693 on GenesisL1: 3D…
- PDB
- 3MLR
- Type
- protein
- Length
- 459 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Human monoclonal anti-HIV-1 GP120 V3 antibody 2557 Fab light chain; Human monoclonal…
- UniProt
- P12490
- Pockets
- 5 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Human monoclonal anti-HIV-1 GP120 V3 antibody 2557 Fab light chain | protein | 219 | 7% helix, 51% strand | — |
| H | Human monoclonal anti-HIV-1 GP120 V3 antibody 2557 Fab heavy chain | protein | 226 | 8% helix, 54% strand | — |
| P | HIV-1 GP120 third variable region (V3) crown | protein | 14 | 0% helix, 50% strand | P12490 |
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 | 303 | 0.52 | 0.74 | 51 | empty |
| 2 | 69 | 0.45 | 0.83 | 19 | empty |
| 3 | 96 | 0.39 | 0.76 | 24 | empty |
| 4 | 70 | 0.39 | 0.78 | 11 | empty |
| 5 | 96 | 0.34 | 0.74 | 21 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1975 Ų buried · 19 hydrogen bonds · protein-protein
- H–P · 427 Ų buried · 10 hydrogen bonds · protein-protein
- L–P · 405 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3MLR · Crystal structure of anti-HIV-1 V3 Fab 2557 in complex with a NY5 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
- Every structure of UniProt P12490
- Elsewhere: RCSB PDB 3MLR · PDBe 3MLR · UniProt P12490
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