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Crystal structure of anti-HIV-1 V3 Fab 1006-15D in complex with an mn V3 peptide
Analyse Crystal structure of anti-HIV-1 V3 Fab 1006-15D in complex with an mn V3 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MLW
- Type
- protein
- Length
- 920 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Human monoclonal anti-HIV-1 GP120 V3 antibody 1006-15D Fab light chain; Human monoclonal…
- UniProt
- P05877
- Ligands
- PO4
- Pockets
- 9 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, M | Human monoclonal anti-HIV-1 GP120 V3 antibody 1006-15D Fab light chain | protein | 215 | 7% helix, 52% strand | — |
| H, I | Human monoclonal anti-HIV-1 GP120 V3 antibody 1006-15D Fab heavy chain | protein | 228 | 8% helix, 52% strand | — |
| P | HIV-1 GP120 third variable region (V3) crown | protein | 17 | 0% helix, 41% strand | P05877 |
| Q | HIV-1 GP120 third variable region (V3) crown | protein | 17 | 0% helix, 41% strand | P05877 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 6 copies · chains L, H, P, M, I, Q
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 742 | 0.67 | 0.75 | 79 | PO4 |
| 2 | 624 | 0.64 | 0.75 | 65 | empty |
| 3 | 158 | 0.48 | 0.78 | 28 | empty |
| 4 | 139 | 0.46 | 0.77 | 27 | empty |
| 5 | 128 | 0.44 | 0.76 | 20 | empty |
Interfaces
7 interfaces between chains.
- M–I · 2084 Ų buried · 20 hydrogen bonds · protein-protein
- L–H · 1976 Ų buried · 19 hydrogen bonds · protein-protein
- H–I · 806 Ų buried · 17 hydrogen bonds · protein-protein
- I–Q · 485 Ų buried · 4 hydrogen bonds · protein-protein
- H–P · 463 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3MLW · Crystal structure of anti-HIV-1 V3 Fab 1006-15D in complex with an MN 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 P05877
- Elsewhere: RCSB PDB 3MLW · PDBe 3MLW · UniProt P05877
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