Research workbench
Crystal structure of clade A/E 93TH057 HIV-1 GP120 core in complex with mae-II-167
Analyse Crystal structure of clade A/E 93TH057 HIV-1 GP120 core in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DVW
- Type
- protein
- Length
- 678 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Clade A/E 93TH057 HIV-1 GP120 core
- UniProt
- A0A0M3KKW9
- Ligands
- 0M4, NAG
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Clade A/E 93TH057 HIV-1 GP120 core | protein | 339 | 18% helix, 38% strand | A0A0M3KKW9 |
Ligands and binding sites
- 0M4 · N-(4-chloro-3-fluorophenyl)-N'-[(3aS,6aS)-hexahydrocyclopenta[c]pyrrol-3a(1H)-ylmethyl]ethanediamide · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 802 | 0.76 | 0.80 | 102 | NAG |
| 2 | 120 | 0.64 | 0.88 | 29 | 0M4 |
| 3 | 89 | 0.60 | 0.88 | 22 | 0M4 |
| 4 | 64 | 0.51 | 0.85 | 18 | NAG |
| 5 | 54 | 0.40 | 0.82 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 472 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 glycan, 14 disulfide (N-glycosylation, disulfide).
Compared structures
- 4DVW · Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with MAE-II-167 · 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
- Every structure of UniProt A0A0M3KKW9
- Elsewhere: RCSB PDB 4DVW · PDBe 4DVW · UniProt A0A0M3KKW9
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