Research workbench
Crystal structure of clade A/E 93TH057 HIV-1 GP120 core in complex with aws-I-169
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
- 4DKR
- Type
- protein
- Length
- 678 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 GP120 core
- Ligands
- 0LJ, NAG
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 17% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | HIV-1 GP120 core | protein | 339 | 17% helix, 37% strand | — |
Ligands and binding sites
- 0LJ · N-[(1R,2R)-2-carbamimidamido-2,3-dihydro-1H-inden-1-yl]-N'-(4-chloro-3-fluorophenyl)ethanediamide · ligand · 2 copies · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 22 copies · chains A, C
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 721 | 0.77 | 0.82 | 89 | NAG |
| 2 | 88 | 0.64 | 0.90 | 23 | 0LJ |
| 3 | 73 | 0.57 | 0.88 | 19 | 0LJ |
| 4 | 64 | 0.49 | 0.84 | 17 | NAG |
| 5 | 57 | 0.44 | 0.83 | 21 | empty |
Interfaces
1 interface between chains.
- A–C · 469 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 glycan, 14 disulfide (N-glycosylation, disulfide).
Compared structures
- 4DKR · Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with AWS-I-169 · 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 4DKR · PDBe 4DKR
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