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Crystal structure of clade A/E 93TH057 HIV-1 GP120 H375S core in complex with dmj-II-121
Analyse Crystal structure of clade A/E 93TH057 HIV-1 GP120 H375S 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
- 4I54
- Type
- protein
- Length
- 678 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 glycoprotein
- Ligands
- 1C1, NAG
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | HIV-1 glycoprotein | protein | 339 | 19% helix, 37% 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 · 16 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
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 742 | 0.75 | 0.80 | 89 | NAG |
| 2 | 79 | 0.62 | 0.90 | 22 | 1C1 |
| 3 | 62 | 0.61 | 0.91 | 20 | empty |
| 4 | 88 | 0.56 | 0.86 | 19 | 1C1 |
| 5 | 59 | 0.55 | 0.88 | 18 | NAG |
Interfaces
1 interface between chains.
- A–B · 502 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 glycan, 14 disulfide (N-glycosylation, disulfide).
Compared structures
- 4I54 · Crystal structure of clade A/E 93TH057 HIV-1 gp120 H375S 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 4I54 · PDBe 4I54
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