Research workbench
Pyrococcus abyssi B family DNA polymerase (triple mutant) bound to a dsdna, in edition mode
Analyse Pyrococcus abyssi B family DNA polymerase (triple mutant) bound to a dsdna, in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FM2
- Type
- protein + DNA
- Length
- 776 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
- 11 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 42% 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 | 753 | 42% helix, 23% strand | P0CL77 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 642 | 0.82 | 0.87 | 72 | empty |
| 2 | 250 | 0.79 | 0.92 | 40 | empty |
| 3 | 332 | 0.69 | 0.83 | 36 | MG |
| 4 | 91 | 0.52 | 0.84 | 19 | empty |
| 5 | 151 | 0.51 | 0.78 | 18 | empty |
Interfaces
3 interfaces between chains.
- T–A · 1444 Ų buried · 34 hydrogen bonds · protein-nucleic
- P–A · 563 Ų buried · 15 hydrogen bonds · protein-nucleic
- T–P · 394 Ų buried · 37 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4FM2 · Pyrococcus abyssi B family DNA polymerase (triple mutant) bound to a dsDNA, in edition… · 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 4FM2 · PDBe 4FM2 · UniProt P0CL77
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