Research workbench
Sivrcm intasome (Q148H/G140S) in complex with bictegravir
Analyse Sivrcm intasome (Q148H/G140S) in complex with bictegravir in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RWO
- Type
- protein + DNA
- Length
- 2,162 residues
- Chains
- 16
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pol protein; DNA (5'- D(*AP*AP*CP*TP*GP*GP*TP*AP*GP*AP*GP*AP*TP*TP*TP*TP*TP*CP*TP*TP*AP*GP…
- UniProt
- E1ANT8
- Ligands
- KLQ, ZN, MG, CL
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 8 distinct chains · 45% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, I | Pol protein | protein | 270 | 43% helix, 22% strand | E1ANT8 |
| Q, S | DNA (5'- D(*AP*AP*CP*TP*GP*GP*TP*AP*GP*AP*GP*AP*TP*TP*TP*TP*TP*CP*TP*TP*AP*GP* C)-3') | dna | 23 | — | — |
| W, T | DNA (5'- D(P*GP*CP*TP*AP*AP*GP*AP*AP*AP*AP*AP*TP*CP*TP*CP*TP*AP*CP*CP*A)-3') | dna | 20 | — | — |
| E, M | Pol protein | protein | 47 | 66% helix, 0% strand | E1ANT8 |
| N, F | Pol protein | protein | 69 | 29% helix, 41% strand | E1ANT8 |
| L, D | Pol protein | protein | 207 | 40% helix, 28% strand | E1ANT8 |
| K, C | Pol protein | protein | 193 | 53% helix, 17% strand | E1ANT8 |
| J, B | Pol protein | protein | 252 | 46% helix, 25% strand | E1ANT8 |
Ligands and binding sites
- KLQ · Bictegravir · ligand · 2 copies · chains A, S, T, Q, W, I
- ZN · Zinc ion · metal · 8 copies · chains A, E, K, J, I, M, C, B
- MG · Magnesium ion · metal · 4 copies · chains A, I
- CL · Chloride ion · ion · 2 copies · chains A, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 913 | 0.84 | 0.86 | 85 | empty |
| 2 | 881 | 0.83 | 0.86 | 80 | empty |
| 3 | 830 | 0.80 | 0.83 | 80 | empty |
| 4 | 645 | 0.78 | 0.83 | 62 | empty |
| 5 | 523 | 0.74 | 0.82 | 40 | empty |
Interfaces
55 interfaces between chains.
- L–I · 1692 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 1688 Ų buried · 11 hydrogen bonds · protein-protein
- D–C · 1622 Ų buried · 11 hydrogen bonds · protein-protein
- L–K · 1618 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1536 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6RWO · SIVrcm intasome (Q148H/G140S) in complex with bictegravir · 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 E1ANT8
- Elsewhere: RCSB PDB 6RWO · PDBe 6RWO · UniProt E1ANT8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.