MolNFT v1 · #157266 · protein
Crystal structure of VRC42.04 Fab in complex with GP41 peptide
6MTP · Antibody VRC42.04 Fab light chain: “Crystal structure of VRC42.04 Fab in complex with GP41 peptide”. X-ray diffraction, 11 pockets (best druggability 0.66). MolNFT v1 #157266 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6MTP
- Type
- protein
- Length
- 896 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody VRC42.04 Fab light chain; Antibody VRC42.04 Fab heavy chain; RV217 founder virus…
- UniProt
- A7L302
- Pockets
- 11 · best druggability 0.66
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, B | Antibody VRC42.04 Fab light chain | protein | 214 | 6% helix, 53% strand | — |
| H | Antibody VRC42.04 Fab heavy chain | protein | 218 | 9% helix, 54% strand | — |
| A | Antibody VRC42.04 Fab heavy chain | protein | 217 | 9% helix, 55% strand | — |
| P | RV217 founder virus GP41 peptide | protein | 18 | 67% helix, 0% strand | A7L302 |
| Q | RV217 founder virus GP41 peptide | protein | 15 | 80% helix, 0% strand | A7L302 |
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 782 | 0.66 | 0.74 | 90 | empty |
| 2 | 358 | 0.56 | 0.75 | 46 | empty |
| 3 | 59 | 0.56 | 0.89 | 21 | empty |
| 4 | 167 | 0.44 | 0.75 | 22 | empty |
| 5 | 95 | 0.40 | 0.77 | 17 | empty |
Interfaces
7 interfaces between chains.
- L–H · 1637 Ų buried · 12 hydrogen bonds · protein-protein
- B–A · 1567 Ų buried · 11 hydrogen bonds · protein-protein
- A–Q · 606 Ų buried · 3 hydrogen bonds · protein-protein
- H–P · 599 Ų buried · 3 hydrogen bonds · protein-protein
- L–B · 403 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6MTP · Crystal structure of VRC42.04 Fab in complex with gp41 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 A7L302
- Elsewhere: RCSB PDB 6MTP · PDBe 6MTP · UniProt A7L302
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