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Crystal structure of HIV-1 LM/HT clade A/E CRF01 GP120 core in complex with (S)-mcg-III-027-D05.
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
- 6ONV
- Type
- protein
- Length
- 337 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 LM/HT clade A/E CRF01 GP120
- UniProt
- A0A0M3KKW9
- Ligands
- MWA, NAG
- Pockets
- 5 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HIV-1 LM/HT clade A/E CRF01 GP120 | protein | 337 | 14% helix, 34% strand | A0A0M3KKW9 |
Ligands and binding sites
- MWA · (3S)-N-(4-chloro-3-fluorophenyl)-1-(methylsulfonyl) piperidine-3-carboxamide · 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
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 | 68 | 0.57 | 0.88 | 18 | MWA |
| 2 | 82 | 0.57 | 0.87 | 20 | empty |
| 3 | 88 | 0.51 | 0.83 | 19 | NAG |
| 4 | 54 | 0.39 | 0.81 | 18 | empty |
| 5 | 80 | 0.36 | 0.76 | 16 | empty |
Modifications
Observed in the structure: 10 glycan, 8 disulfide (N-glycosylation, disulfide).
Compared structures
- 6ONV · 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 6ONV · PDBe 6ONV · UniProt A0A0M3KKW9
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