MolNFT v1 · #27376 · protein + DNA
PHI29 DNA polymerase, orthorhombic crystal form, ssdna complex
1XHZ · 5'-D(*TP*TP*TP*TP*T)-3': “PHI29 DNA polymerase, orthorhombic crystal form, ssdna complex”. X-ray diffraction, 20 pockets (best druggability 0.74). MolNFT v1 #27376 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1XHZ
- Type
- protein + DNA
- Length
- 2,301 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*TP*TP*TP*TP*T)-3'; DNA polymerase
- EC
- 2.7.7.7
- UniProt
- P03680
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, G, H | 5'-D(*TP*TP*TP*TP*T)-3' | dna | 5 | — | — |
| F | 5'-D(*TP*TP*TP*TP*T)-3' | dna | 2 | — | — |
| A, B, C, D | DNA polymerase (EC 2.7.7.7) | protein | 571 | 28% helix, 32% strand | P03680 |
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 805 | 0.74 | 0.79 | 51 | empty |
| 2 | 805 | 0.73 | 0.78 | 81 | empty |
| 3 | 362 | 0.72 | 0.84 | 52 | empty |
| 4 | 656 | 0.69 | 0.77 | 57 | empty |
| 5 | 51 | 0.68 | 0.97 | 16 | empty |
Interfaces
7 interfaces between chains.
- C–D · 932 Ų buried · 15 hydrogen bonds · protein-protein
- E–A · 763 Ų buried · 12 hydrogen bonds · protein-nucleic
- H–D · 763 Ų buried · 13 hydrogen bonds · protein-nucleic
- G–C · 755 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–B · 663 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 1XHZ · Phi29 DNA polymerase, orthorhombic crystal form, ssDNA complex · the same entry in another collection · chain E against E, 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 1XHZ · PDBe 1XHZ · UniProt P03680
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