Research workbench
Mper-tmd of HIV-1 env bound with the entry inhibitor S2C3
Analyse Mper-tmd of HIV-1 env bound with the entry inhibitor S2C3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6V4T
- Type
- protein
- Length
- 153 residues
- Chains
- 3
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP160
- UniProt
- Q74849
- Ligands
- QOJ
- Pockets
- 2 · best druggability 0.76
Structure
solution nmr · 1 distinct chain · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Envelope glycoprotein GP160 | protein | 51 | 73% helix, 0% strand | Q74849 |
Ligands and binding sites
- QOJ · 4-[10-(9-azanyl-2,3-dihydro-1~{H}-cyclopenta[b]quinolin-4-yl)decyl]-2,3-dihydro-1~{H}-cyclopenta[b]quinolin-9-amine · ligand · 3 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 942 | 0.76 | 0.78 | 65 | QOJ |
| 2 | 130 | 0.66 | 0.88 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–C · 754 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 703 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 661 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6V4T · MPER-TMD of HIV-1 Env bound with the entry inhibitor S2C3 · 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 Q74849
- Elsewhere: RCSB PDB 6V4T · PDBe 6V4T · UniProt Q74849
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