MolNFT v1 · #138260 · protein
Crystal structure of 10E8V4-5R+100CF Fab in complex with HIV-1 GP41 peptide
5WDF · 10E8V4-5R+100CF Fab heavy chain: “Crystal structure of 10E8V4-5R+100CF Fab in complex with HIV-1 GP41 peptide”. X-ray diffraction, 12 pockets (best druggability 0.78). MolNFT v1 #138260 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5WDF
- Type
- protein
- Length
- 848 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 10E8V4-5R+100CF Fab heavy chain; FA10E8V4-5R+100CF Fab light chain; HIV-1 GP41 peptide
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 8% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | 10E8V4-5R+100CF Fab heavy chain | protein | 209 | 3% helix, 50% strand | — |
| L | FA10E8V4-5R+100CF Fab light chain | protein | 206 | 7% helix, 50% strand | — |
| A | 10E8V4-5R+100CF Fab heavy chain | protein | 202 | 4% helix, 48% strand | — |
| B | FA10E8V4-5R+100CF Fab light chain | protein | 198 | 6% helix, 48% strand | — |
| P | HIV-1 GP41 peptide | protein | 17 | 65% helix, 0% strand | — |
| Q | HIV-1 GP41 peptide | protein | 16 | 75% helix, 0% strand | — |
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 679 | 0.78 | 0.83 | 73 | empty |
| 2 | 813 | 0.72 | 0.78 | 78 | empty |
| 3 | 133 | 0.55 | 0.83 | 17 | empty |
| 4 | 164 | 0.50 | 0.77 | 28 | empty |
| 5 | 53 | 0.49 | 0.87 | 16 | empty |
Interfaces
12 interfaces between chains.
- H–L · 2082 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1947 Ų buried · 16 hydrogen bonds · protein-protein
- H–A · 657 Ų buried · 10 hydrogen bonds · protein-protein
- H–P · 652 Ų buried · 6 hydrogen bonds · protein-protein
- A–Q · 620 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 5WDF · Crystal structure of 10E8v4-5R+100cF Fab in complex with HIV-1 gp41 peptide · the same entry in another collection · chain H against H, 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 5WDF · PDBe 5WDF
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