Research workbench
PHI29 DNA polymerase complexed with single-stranded DNA
Analyse PHI29 DNA polymerase complexed with single-stranded DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PY5
- Type
- protein + DNA
- Length
- 1,152 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(GGACTTT)-3'; DNA polymerase
- EC
- 2.7.7.7
- UniProt
- P03680
- Pockets
- 17 · best druggability 0.75
Structure
x-ray diffraction · 6 distinct chains · 30% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| J | 5'-D(GGACTTT)-3' | dna | 6 | — | — |
| Y, E | 5'-D(GGACTTT)-3' | dna | 5 | — | — |
| D | 5'-D(GGACTTT)-3' | dna | 6 | — | — |
| L | 5'-D(GGACTTT)-3' | dna | 4 | — | — |
| A | DNA polymerase (EC 2.7.7.7) | protein | 564 | 30% helix, 35% strand | P03680 |
| B | DNA polymerase (EC 2.7.7.7) | protein | 562 | 30% helix, 35% strand | P03680 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 27 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 554 | 0.75 | 0.83 | 71 | empty |
| 2 | 304 | 0.72 | 0.86 | 41 | empty |
| 3 | 240 | 0.72 | 0.88 | 37 | empty |
| 4 | 740 | 0.71 | 0.78 | 80 | EDO |
| 5 | 179 | 0.70 | 0.88 | 38 | empty |
Interfaces
9 interfaces between chains.
- D–A · 771 Ų buried · 11 hydrogen bonds · protein-nucleic
- J–A · 699 Ų buried · 7 hydrogen bonds · protein-nucleic
- E–B · 659 Ų buried · 7 hydrogen bonds · protein-nucleic
- L–B · 658 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–B · 634 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 2PY5 · Phi29 DNA polymerase complexed with single-stranded DNA · the same entry in another collection · chain J against J, 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 2PY5 · PDBe 2PY5 · UniProt P03680
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