Research workbench
Crystal structure of the T7 replisome in the absence of DNA
Analyse Crystal structure of the T7 replisome in the absence of DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IKN
- Type
- protein
- Length
- 5,604 residues
- Chains
- 13
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed DNA polymerase; DNA PRIMASE/HELICASE; Thioredoxin-1
- EC
- 2.7.7.7, 3.1.11.-, 2.7.7.-, 3.6.4.12
- UniProt
- P00581, P03692, P0AA27
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 9 distinct chains · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed DNA polymerase (EC 2.7.7.7, 3.1.11.-) | protein | 639 | 48% helix, 12% strand | P00581 |
| B | DNA-directed DNA polymerase (EC 2.7.7.7, 3.1.11.-) | protein | 636 | 49% helix, 12% strand | P00581 |
| C | DNA-directed DNA polymerase (EC 2.7.7.7, 3.1.11.-) | protein | 633 | 50% helix, 12% strand | P00581 |
| D, E | DNA PRIMASE/HELICASE (EC 2.7.7.-, 3.6.4.12) | protein | 485 | 31% helix, 21% strand | P03692 |
| F, H | DNA PRIMASE/HELICASE (EC 2.7.7.-, 3.6.4.12) | protein | 486 | 29% helix, 21% strand | P03692 |
| G | DNA PRIMASE/HELICASE (EC 2.7.7.-, 3.6.4.12) | protein | 484 | 32% helix, 21% strand | P03692 |
| I | DNA PRIMASE/HELICASE (EC 2.7.7.-, 3.6.4.12) | protein | 472 | 31% helix, 20% strand | P03692 |
| J | DNA PRIMASE/HELICASE (EC 2.7.7.-, 3.6.4.12) | protein | 483 | 33% helix, 22% strand | P03692 |
| K, L, M | Thioredoxin-1 | protein | 105 | 35% helix, 28% strand | P0AA27 |
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 | 533 | 0.84 | 0.90 | 81 | empty |
| 2 | 825 | 0.84 | 0.87 | 92 | empty |
| 3 | 539 | 0.82 | 0.88 | 68 | empty |
| 4 | 730 | 0.82 | 0.86 | 86 | empty |
| 5 | 712 | 0.81 | 0.85 | 82 | empty |
Interfaces
17 interfaces between chains.
- F–G · 2676 Ų buried · 27 hydrogen bonds · protein-protein
- D–J · 2422 Ų buried · 38 hydrogen bonds · protein-protein
- D–E · 2326 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 2259 Ų buried · 23 hydrogen bonds · protein-protein
- G–H · 2167 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5IKN · Crystal Structure of the T7 Replisome in the Absence of DNA · the same entry in another collection · chain M against M, 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 P00581
- Every structure of UniProt P03692
- Every structure of UniProt P0AA27
- Elsewhere: RCSB PDB 5IKN · PDBe 5IKN · UniProt P00581 · UniProt P03692 · UniProt P0AA27
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