MolNFT v1 · #94720 · protein
Crystal structure of clade C1086 HIV-1 GP120 core in complex with dmj- II-121
4I53 · HIV-1 glycoprotein: “Crystal structure of clade C1086 HIV-1 GP120 core in complex with dmj- II-121”. X-ray diffraction, 2 ligands (1C1, NAG), 5 pockets (best druggability 0.75). MolNFT v1 #94720 on GenesisL1: 3D structure, binding…
- PDB
- 4I53
- Type
- protein
- Length
- 671 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 glycoprotein
- Ligands
- 1C1, NAG
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HIV-1 glycoprotein | protein | 336 | 18% helix, 39% strand | — |
| B | HIV-1 glycoprotein | protein | 335 | 18% helix, 39% strand | — |
Ligands and binding sites
- 1C1 · amino({[(1R,2R)-1-({[(4-chloro-3-fluorophenyl)amino](oxo)acetyl}amino)-2,3-dihydro-1H-inden-2-yl]methyl}amino)methanimi nium · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, B
- FMT · Formic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 935 | 0.75 | 0.78 | 112 | NAG |
| 2 | 73 | 0.56 | 0.87 | 19 | 1C1 |
| 3 | 66 | 0.55 | 0.88 | 19 | 1C1 |
| 4 | 130 | 0.53 | 0.81 | 22 | NAG |
| 5 | 50 | 0.40 | 0.81 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 340 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 14 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 4I53 · Crystal structure of clade C1086 HIV-1 gp120 core in complex with DMJ-II-121 · the same entry in another collection · chain A against A, 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 4I53 · PDBe 4I53
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