MolNFT v1 · #116899 · protein
Crystal structure of anti-HIV-1 antibody F240 Fab in complex with GP41 peptide
5DRZ · HIV antibody F240 light chain: “Crystal structure of anti-HIV-1 antibody F240 Fab in complex with GP41 peptide”. X-ray diffraction, 1 ligand (MG), 11 pockets (best druggability 0.63). MolNFT v1 #116899 on GenesisL1: 3D structure…
- PDB
- 5DRZ
- Type
- protein
- Length
- 918 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV antibody F240 light chain; HIV antibody F240 heavy chain; Envelope glycoprotein GP160
- UniProt
- P03378
- Ligands
- MG
- Pockets
- 11 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | HIV antibody F240 light chain | protein | 216 | 5% helix, 52% strand | — |
| H, B | HIV antibody F240 heavy chain | protein | 227 | 5% helix, 54% strand | — |
| A | HIV antibody F240 light chain | protein | 218 | 5% helix, 52% strand | — |
| Q, P | Envelope glycoprotein GP160 | protein | 15 | 0% helix, 27% strand | P03378 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 605 | 0.63 | 0.74 | 57 | empty |
| 2 | 551 | 0.62 | 0.75 | 63 | empty |
| 3 | 166 | 0.46 | 0.76 | 26 | empty |
| 4 | 163 | 0.45 | 0.75 | 35 | empty |
| 5 | 145 | 0.42 | 0.74 | 27 | empty |
Interfaces
10 interfaces between chains.
- L–H · 2007 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1987 Ų buried · 18 hydrogen bonds · protein-protein
- B–Q · 537 Ų buried · 15 hydrogen bonds · protein-protein
- H–P · 524 Ų buried · 15 hydrogen bonds · protein-protein
- Q–P · 354 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 5DRZ · Crystal structure of anti-HIV-1 antibody F240 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 P03378
- Elsewhere: RCSB PDB 5DRZ · PDBe 5DRZ · UniProt P03378
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