MolNFT v1 · #66153 · protein
Structure of HIV-1 GP120 (core with V3) in complex with CD4-binding- site antibody F105
3HI1 · Glycoprotein 120: “Structure of HIV-1 GP120 (core with V3) in complex with CD4-binding- site antibody F105”. X-ray diffraction, 1 ligand (NAG), 20 pockets (best druggability 0.81). MolNFT v1 #66153 on GenesisL1: 3D structure…
- PDB
- 3HI1
- Type
- protein
- Length
- 1,458 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoprotein 120; F105 light chain; F105 heavy chain
- UniProt
- P35961
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G, J | Glycoprotein 120 | protein | 289 | 17% helix, 34% strand | P35961 |
| L, A | F105 light chain | protein | 215 | 5% helix, 56% strand | — |
| H, B | F105 heavy chain | protein | 225 | 9% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 27 copies · chains G, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 812 | 0.81 | 0.84 | 93 | NAG |
| 2 | 403 | 0.76 | 0.86 | 64 | empty |
| 3 | 540 | 0.59 | 0.73 | 54 | empty |
| 4 | 188 | 0.59 | 0.82 | 27 | empty |
| 5 | 226 | 0.58 | 0.79 | 33 | empty |
Interfaces
7 interfaces between chains.
- G–J · 2002 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1953 Ų buried · 16 hydrogen bonds · protein-protein
- L–H · 1946 Ų buried · 16 hydrogen bonds · protein-protein
- G–H · 871 Ų buried · 13 hydrogen bonds · protein-protein
- J–B · 849 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 glycan, 20 disulfide (N-glycosylation, disulfide).
Compared structures
- 3HI1 · Structure of HIV-1 gp120 (core with V3) in Complex with CD4-Binding-Site Antibody F105 · 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 P35961
- Elsewhere: RCSB PDB 3HI1 · PDBe 3HI1 · UniProt P35961
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