Research workbench
Crystal structure of anti-HIV-1 V3 Fab 2557 in complex with a UG1033 V3 peptide
Analyse Crystal structure of anti-HIV-1 V3 Fab 2557 in complex with a UG1033 V3 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MLT
- Type
- protein
- Length
- 1,757 residues
- Chains
- 10
- 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
- Q9WNX3
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 6 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Human monoclonal anti-HIV-1 GP120 V3 antibody 2557 Fab light chain | protein | 216 | 7% helix, 51% strand | — |
| H | Human monoclonal anti-HIV-1 GP120 V3 antibody 2557 Fab heavy chain | protein | 215 | 7% helix, 53% strand | — |
| P, C | HIV-1 GP120 third variable region (V3) crown | protein | 14 | 0% helix, 50% strand | Q9WNX3 |
| A | Human monoclonal anti-HIV-1 GP120 V3 antibody 2557 Fab light chain | protein | 215 | 7% helix, 48% strand | — |
| B, E, I | Human monoclonal anti-HIV-1 GP120 V3 antibody 2557 Fab heavy chain | protein | 219 | 8% helix, 54% strand | — |
| D, G | Human monoclonal anti-HIV-1 GP120 V3 antibody 2557 Fab light chain | protein | 213 | 6% helix, 50% strand | — |
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1066 | 0.72 | 0.76 | 111 | empty |
| 2 | 1016 | 0.70 | 0.74 | 108 | empty |
| 3 | 676 | 0.67 | 0.76 | 89 | empty |
| 4 | 803 | 0.66 | 0.74 | 96 | empty |
| 5 | 443 | 0.58 | 0.74 | 49 | empty |
Interfaces
16 interfaces between chains.
- A–B · 1871 Ų buried · 13 hydrogen bonds · protein-protein
- L–H · 1842 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 1822 Ų buried · 12 hydrogen bonds · protein-protein
- G–I · 1803 Ų buried · 13 hydrogen bonds · protein-protein
- H–E · 851 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 3MLT · Crystal structure of anti-HIV-1 V3 Fab 2557 in complex with a UG1033 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 Q9WNX3
- Elsewhere: RCSB PDB 3MLT · PDBe 3MLT · UniProt Q9WNX3
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