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Crystal structure of HIV-1 LM/HT clade A/E CRF01 GP120 core in complex with (S)-mcg-III-188-A02.
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
- 6ONF
- Type
- protein
- Length
- 340 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
- MW4, NAG
- Pockets
- 2 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 17% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Clade A/E 93TH057 HIV-1 GP120 core | protein | 340 | 17% helix, 36% strand | A0A0M3KKW9 |
Ligands and binding sites
- MW4 · Ethyl (3S)-3-[(4-chloro-3-fluorophenyl) carbamoyl]piperidine-1-carboxylate · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 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
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 68 | 0.56 | 0.88 | 18 | MW4 |
| 2 | 59 | 0.49 | 0.85 | 18 | NAG |
Modifications
Observed in the structure: 10 glycan, 8 disulfide (N-glycosylation, disulfide).
Compared structures
- 6ONF · 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 6ONF · PDBe 6ONF · UniProt A0A0M3KKW9
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