Research workbench
PHI29 DNA polymerase, orthorhombic crystal form
Analyse PHI29 DNA polymerase, orthorhombic crystal form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XHX
- Type
- protein
- Length
- 2,284 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase
- EC
- 2.7.7.7
- UniProt
- P03680
- Ligands
- MG, SO4
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | DNA polymerase (EC 2.7.7.7) | protein | 571 | 29% helix, 34% strand | P03680 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 778 | 0.73 | 0.79 | 88 | empty |
| 2 | 436 | 0.71 | 0.81 | 68 | empty |
| 3 | 697 | 0.70 | 0.77 | 59 | empty |
| 4 | 51 | 0.69 | 0.97 | 15 | empty |
| 5 | 743 | 0.68 | 0.76 | 70 | empty |
Interfaces
3 interfaces between chains.
- C–D · 939 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 632 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 425 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1XHX · Phi29 DNA Polymerase, orthorhombic crystal form · 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 P03680
- Elsewhere: RCSB PDB 1XHX · PDBe 1XHX · UniProt P03680
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