MolNFT v1 · #182921 · protein
Rhesusized RV305 DH677.3 Fab bound to clade A/E 93TH057 HIV-1 GP120 core.
7N8Q: “Rhesusized RV305 DH677.3 Fab bound to clade A/E 93TH057 HIV-1 GP120 core.”. X-ray diffraction, 3 ligands (MPT, NAG, NH2), 20 pockets (best druggability 0.76). MolNFT v1 #182921 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 7N8Q
- Type
- protein
- Length
- 1,527 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Clade A/E 93TH057 HIV-1 GP120 core; M48U1 CD4 mimetic peptide; Rhesusized DH677.3 Fab…
- UniProt
- A0A0M3KKW9
- Ligands
- MPT, NAG, NH2
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 6 distinct chains · 9% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Clade A/E 93TH057 HIV-1 GP120 core | protein | 338 | 13% helix, 34% strand | A0A0M3KKW9 |
| N | M48U1 CD4 mimetic peptide | protein | 26 | 38% helix, 23% strand | — |
| H | Rhesusized DH677.3 Fab heavy chain | protein | 218 | 1% helix, 45% strand | — |
| L, D | Rhesusized DH677.3 Fab light chain | protein | 210 | 4% helix, 33% strand | — |
| A | Clade A/E 93TH057 HIV-1 GP120 core | protein | 308 | 15% helix, 29% strand | A0A0M3KKW9 |
| C | Rhesusized DH677.3 Fab heavy chain | protein | 217 | 3% helix, 45% strand | — |
Ligands and binding sites
- MPT · Beta-mercaptopropionic acid · ligand · chains G, N
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains G, A
- NH2 · Amino group · ion · chains N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 871 | 0.76 | 0.80 | 94 | NAG |
| 2 | 280 | 0.64 | 0.81 | 46 | empty |
| 3 | 531 | 0.60 | 0.74 | 63 | empty |
| 4 | 66 | 0.59 | 0.90 | 19 | NAG |
| 5 | 199 | 0.56 | 0.80 | 37 | empty |
Interfaces
12 interfaces between chains.
- C–D · 1879 Ų buried · 13 hydrogen bonds · protein-protein
- H–L · 1849 Ų buried · 14 hydrogen bonds · protein-protein
- G–N · 742 Ų buried · 4 hydrogen bonds · protein-protein
- G–L · 500 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 463 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 disulfide, 18 glycan, 2 covalent, 1 d-amino, 1 modified (disulfide, N-glycosylation, covalent ligand, D-amino acid, nonstandard).
Compared structures
- 7N8Q · Rhesusized RV305 DH677.3 Fab bound to Clade A/E 93TH057 HIV-1 gp120 core. · the same entry in another collection · chain G against G, 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 A0A0M3KKW9
- Elsewhere: RCSB PDB 7N8Q · PDBe 7N8Q · UniProt A0A0M3KKW9
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