MolNFT v1 · #136879 · protein
Crystal structure of rabbit anti-HIV-1 GP120 V3 Fab 10A37 in complex with V3 peptide jr-fl
5V6L · Light chain of Fab fragment of rabbit anti-HIV1 GP120 V3…: “Crystal structure of rabbit anti-HIV-1 GP120 V3 Fab 10A37 in complex with V3 peptide jr-fl”. X-ray diffraction, 10 pockets (best druggability 0.73). MolNFT v1 #136879 on…
- PDB
- 5V6L
- Type
- protein
- Length
- 898 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light chain of Fab fragment of rabbit anti-HIV1 GP120 V3 mab 10A37; Heavy chain of Fab…
- UniProt
- Q85825
- Pockets
- 10 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, M | Light chain of Fab fragment of rabbit anti-HIV1 GP120 V3 mab 10A37 | protein | 215 | 8% helix, 53% strand | — |
| H | Heavy chain of Fab fragment of rabbit anti-HIV1 GP120 V3 mab 10A37 | protein | 220 | 4% helix, 52% strand | — |
| P | Envelope glycoprotein, V3 region | protein | 14 | 43% helix, 0% strand | Q85825 |
| I | Heavy chain of Fab fragment of rabbit anti-HIV1 GP120 V3 mab 10A37 | protein | 218 | 6% helix, 51% strand | — |
| Q | Envelope glycoprotein, V3 region | protein | 16 | 38% helix, 0% strand | Q85825 |
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 508 | 0.73 | 0.82 | 76 | empty |
| 2 | 480 | 0.62 | 0.76 | 47 | empty |
| 3 | 478 | 0.60 | 0.75 | 54 | empty |
| 4 | 256 | 0.54 | 0.77 | 33 | empty |
| 5 | 222 | 0.51 | 0.76 | 32 | empty |
Interfaces
9 interfaces between chains.
- L–H · 1930 Ų buried · 14 hydrogen bonds · protein-protein
- M–I · 1910 Ų buried · 13 hydrogen bonds · protein-protein
- I–Q · 505 Ų buried · 11 hydrogen bonds · protein-protein
- H–P · 465 Ų buried · 12 hydrogen bonds · protein-protein
- H–I · 370 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 5V6L · Crystal Structure of Rabbit Anti-HIV-1 gp120 V3 Fab 10A37 in complex with V3 peptide JR-FL · 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 Q85825
- Elsewhere: RCSB PDB 5V6L · PDBe 5V6L · UniProt Q85825
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