Research workbench
Crystal structure of T7 endo I resolvase in complex with a holliday junction
Analyse Crystal structure of T7 endo I resolvase in complex with a holliday junction in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PFJ
- Type
- protein + DNA
- Length
- 313 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 27-mer; Endodeoxyribonuclease 1
- EC
- 3.1.21.2
- UniProt
- P00641
- Ligands
- CA
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Z | 27-mer | dna | 27 | — | — |
| Y | 27-mer | dna | 27 | — | — |
| A | Endodeoxyribonuclease 1 (EC 3.1.21.2) | protein | 129 | 31% helix, 26% strand | P00641 |
| B | Endodeoxyribonuclease 1 (EC 3.1.21.2) | protein | 130 | 31% helix, 25% strand | P00641 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains Z, A, B, Y
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 501 | 0.68 | 0.79 | 57 | empty |
| 2 | 395 | 0.64 | 0.79 | 28 | empty |
| 3 | 396 | 0.59 | 0.76 | 38 | empty |
| 4 | 294 | 0.57 | 0.78 | 22 | CA |
| 5 | 226 | 0.53 | 0.77 | 23 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3015 Ų buried · 46 hydrogen bonds · protein-protein
- Z–Y · 701 Ų buried · 47 hydrogen bonds · nucleic-nucleic
- Y–A · 601 Ų buried · 10 hydrogen bonds · protein-nucleic
- Z–B · 587 Ų buried · 15 hydrogen bonds · protein-nucleic
- Y–B · 485 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
- 2PFJ · Crystal Structure of T7 Endo I resolvase in complex with a Holliday Junction · the same entry in another collection · chain Z against Z, 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 P00641
- Elsewhere: RCSB PDB 2PFJ · PDBe 2PFJ · UniProt P00641
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