Research workbench
Pyrococcus abyssi B family DNA polymerase bound to a dsdna, in edition mode
Analyse Pyrococcus abyssi B family DNA polymerase bound to a dsdna, in edition mode in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FM0
- Type
- protein + DNA
- Length
- 777 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Template strand; Primer strand; DNA polymerase 1
- EC
- 2.7.7.7
- UniProt
- P0CL77
- Ligands
- MG
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | Template strand | dna | 15 | — | — |
| P | Primer strand | dna | 8 | — | — |
| A | DNA polymerase 1 (EC 2.7.7.7) | protein | 754 | 41% helix, 23% strand | P0CL77 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1035 | 0.84 | 0.86 | 85 | GOL |
| 2 | 151 | 0.69 | 0.89 | 26 | MG |
| 3 | 425 | 0.69 | 0.80 | 39 | MG |
| 4 | 87 | 0.50 | 0.83 | 18 | empty |
| 5 | 145 | 0.47 | 0.77 | 19 | empty |
Interfaces
3 interfaces between chains.
- T–A · 1414 Ų buried · 35 hydrogen bonds · protein-nucleic
- P–A · 540 Ų buried · 12 hydrogen bonds · protein-nucleic
- T–P · 391 Ų buried · 43 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4FM0 · Pyrococcus abyssi B family DNA polymerase bound to a dsDNA, in edition mode · the same entry in another collection · chain T against T, TM-score 1.00
- P0CL77 · AlphaFold monomer V2.0 prediction for DNA polymerase 1 (P0CL77) · a predicted model of the same protein · chain A against A, TM-score 0.83
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 P0CL77
- Elsewhere: RCSB PDB 4FM0 · PDBe 4FM0 · UniProt P0CL77
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