Research workbench
Crystal structure of clade A/E 93TH057 HIV-1 GP120 core in complex with dmj-I-228
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
- 4DKQ
- Type
- protein
- Length
- 339 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Clade A/E 93TH057 HIV-1 GP120 core
- Ligands
- 0LK, NAG
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Clade A/E 93TH057 HIV-1 GP120 core | protein | 339 | 19% helix, 38% strand | — |
Ligands and binding sites
- 0LK · N-[(1S,2S)-2-carbamimidamido-2,3-dihydro-1H-inden-1-yl]-N'-(4-chloro-3-fluorophenyl)ethanediamide · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.64 | 0.88 | 28 | 0LK |
| 2 | 64 | 0.51 | 0.86 | 17 | NAG |
| 3 | 52 | 0.51 | 0.87 | 16 | empty |
| 4 | 53 | 0.40 | 0.82 | 17 | empty |
| 5 | 64 | 0.33 | 0.76 | 16 | empty |
Modifications
Observed in the structure: 11 glycan, 7 disulfide (N-glycosylation, disulfide).
Compared structures
- 4DKQ · Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with DMJ-I-228 · 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 4DKQ · PDBe 4DKQ
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.