Research workbench
PHI29 DNA polymerase ssdna complex, monoclinic crystal form
Analyse PHI29 DNA polymerase ssdna complex, monoclinic crystal form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XI1
- Type
- protein + DNA
- Length
- 1,148 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(P*TP*TP*TP*TP*T)-3'; DNA polymerase
- EC
- 2.7.7.7
- UniProt
- P03680
- Ligands
- MG
- Pockets
- 18 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | 5'-D(P*TP*TP*TP*TP*T)-3' | dna | 3 | — | — |
| A, B | DNA polymerase (EC 2.7.7.7) | protein | 571 | 30% helix, 34% strand | P03680 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 692 | 0.70 | 0.78 | 71 | empty |
| 2 | 57 | 0.70 | 0.97 | 18 | empty |
| 3 | 468 | 0.68 | 0.79 | 46 | empty |
| 4 | 254 | 0.66 | 0.83 | 28 | empty |
| 5 | 337 | 0.64 | 0.80 | 40 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1379 Ų buried · 7 hydrogen bonds · protein-protein
- C–A · 502 Ų buried · 8 hydrogen bonds · protein-nucleic
- D–B · 499 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 1XI1 · Phi29 DNA polymerase ssDNA complex, monoclinic crystal form · the same entry in another collection · chain C against C, 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 P03680
- Elsewhere: RCSB PDB 1XI1 · PDBe 1XI1 · UniProt P03680
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