Research workbench
Sivrcm intasome
Analyse Sivrcm intasome in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RWL
- 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(P*GP*CP*TP*AP*AP*GP*AP*AP*AP*AP*AP*TP*CP*TP*CP*TP*AP*CP*CP*A)-3')…
- UniProt
- E1ANT8
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 8 distinct chains · 44% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, I | Pol protein | protein | 270 | 42% helix, 21% strand | E1ANT8 |
| B, J | Pol protein | protein | 252 | 45% helix, 25% strand | E1ANT8 |
| C, K | Pol protein | protein | 193 | 53% helix, 17% strand | E1ANT8 |
| D, L | Pol protein | protein | 207 | 39% helix, 29% strand | E1ANT8 |
| F, N | Pol protein | protein | 69 | 29% helix, 45% strand | E1ANT8 |
| M, E | Pol protein | protein | 47 | 66% helix, 0% strand | E1ANT8 |
| T, W | 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 | — | — |
| S, Q | 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 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, M, I, J, K, E
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 | 1000 | 0.84 | 0.85 | 90 | empty |
| 2 | 865 | 0.83 | 0.85 | 84 | empty |
| 3 | 407 | 0.74 | 0.84 | 40 | empty |
| 4 | 706 | 0.74 | 0.80 | 47 | empty |
| 5 | 533 | 0.73 | 0.82 | 46 | empty |
Interfaces
55 interfaces between chains.
- I–L · 1720 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1680 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 1648 Ų buried · 7 hydrogen bonds · protein-protein
- K–L · 1582 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1545 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6RWL · SIVrcm intasome · 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 6RWL · PDBe 6RWL · UniProt E1ANT8
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