MolNFT v1 · #163231 · protein + DNA
Sivrcm intasome in complex with dolutegravir
6RWN · Pol protein: “Sivrcm intasome in complex with dolutegravir”. Electron microscopy, 4 ligands (DLU, ZN, MG), 20 pockets (best druggability 0.84). MolNFT v1 #163231 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6RWN
- 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
- DLU, 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 | 42% helix, 21% 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 | 64% helix, 0% strand | E1ANT8 |
| N, F | Pol protein | protein | 69 | 26% helix, 42% strand | E1ANT8 |
| L, D | Pol protein | protein | 207 | 40% helix, 28% strand | E1ANT8 |
| K, C | Pol protein | protein | 193 | 54% helix, 17% strand | E1ANT8 |
| J, B | Pol protein | protein | 252 | 46% helix, 25% strand | E1ANT8 |
Ligands and binding sites
- DLU · (4r,12as)-N-(2,4-difluorobenzyl)-7-hydroxy-4-methyl-6, 8-dioxo-3,4,6,8,12,12A-hexahydro-2H-pyrido[1',2':4, 5]pyrazino[2,1-b][1,3]oxazine-9-carboxamide · 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 | 1119 | 0.84 | 0.85 | 103 | empty |
| 2 | 910 | 0.83 | 0.85 | 82 | empty |
| 3 | 1071 | 0.78 | 0.80 | 90 | empty |
| 4 | 529 | 0.74 | 0.82 | 42 | empty |
| 5 | 414 | 0.73 | 0.84 | 49 | empty |
Interfaces
57 interfaces between chains.
- L–I · 1696 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 1692 Ų buried · 10 hydrogen bonds · protein-protein
- D–C · 1595 Ų buried · 9 hydrogen bonds · protein-protein
- L–K · 1593 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1539 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6RWN · SIVrcm intasome in complex with dolutegravir · 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 6RWN · PDBe 6RWN · UniProt E1ANT8
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