Research workbench
Crystal structure of HIV-1 LM/HT clade A/E CRF01 GP120 core in complex with (S)-mcg-III-188-A01.
Analyse Crystal structure of HIV-1 LM/HT clade A/E CRF01 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
- 6ONE
- Type
- protein
- Length
- 341 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Clade A/E 93TH057 HIV-1 GP120 core
- UniProt
- A0A0M3KKW9
- Ligands
- MVY, NAG
- Pockets
- 3 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 17% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Clade A/E 93TH057 HIV-1 GP120 core | protein | 341 | 17% helix, 37% strand | A0A0M3KKW9 |
Ligands and binding sites
- MVY · Methyl (3S)-3-[(4-chloro-3-fluorophenyl) carbamoyl]piperidine-1-carboxylate · 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
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 63 | 0.53 | 0.87 | 18 | MVY |
| 2 | 78 | 0.52 | 0.85 | 20 | NAG |
| 3 | 57 | 0.40 | 0.81 | 16 | empty |
Modifications
Observed in the structure: 11 glycan, 8 disulfide (N-glycosylation, disulfide).
Compared structures
- 6ONE · Crystal structure of HIV-1 LM/HT Clade A/E CRF01 gp120 core in complex with… · 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 6ONE · PDBe 6ONE · UniProt A0A0M3KKW9
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