MolNFT v1 · #71694 · protein
Crystal structure of anti-HIV-1 V3 mab 2557 Fab in complex with a HIV- 1 GP120 V3 mimotope
3MLS · Human monoclonal anti-HIV-1 GP120 V3 antibody 2557 Fab…: “Crystal structure of anti-HIV-1 V3 mab 2557 Fab in complex with a HIV- 1 GP120 V3 mimotope”. X-ray diffraction, 20 pockets (best druggability 0.73). MolNFT v1 #71694 on…
- PDB
- 3MLS
- Type
- protein
- Length
- 1,858 residues
- Chains
- 12
- 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…
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, M, N, O | Human monoclonal anti-HIV-1 GP120 V3 antibody 2557 Fab light chain | protein | 219 | 6% helix, 50% strand | — |
| H, I, J | Human monoclonal anti-HIV-1 GP120 V3 antibody 2557 Fab heavy chain | protein | 226 | 9% helix, 54% strand | — |
| P, Q, R, S | Rationally designed V3 mimotope | protein | 20 | 0% helix, 35% strand | — |
| K | Human monoclonal anti-HIV-1 GP120 V3 antibody 2557 Fab heavy chain | protein | 224 | 7% helix, 53% strand | — |
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1050 | 0.73 | 0.76 | 106 | empty |
| 2 | 1135 | 0.72 | 0.76 | 118 | empty |
| 3 | 737 | 0.70 | 0.77 | 80 | empty |
| 4 | 554 | 0.63 | 0.75 | 48 | empty |
| 5 | 518 | 0.62 | 0.75 | 57 | empty |
Interfaces
22 interfaces between chains.
- L–H · 1882 Ų buried · 14 hydrogen bonds · protein-protein
- N–J · 1874 Ų buried · 12 hydrogen bonds · protein-protein
- M–I · 1858 Ų buried · 13 hydrogen bonds · protein-protein
- O–K · 1776 Ų buried · 11 hydrogen bonds · protein-protein
- H–J · 848 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 3MLS · Crystal structure of anti-HIV-1 V3 mAb 2557 Fab in complex with a HIV-1 gp120 V3 mimotope · the same entry in another collection · chain S against S, 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 3MLS · PDBe 3MLS
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