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
- 4FLY
- 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 0.84
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | Template strand | dna | 13 | — | — |
| P | Primer strand | dna | 8 | — | — |
| A | DNA polymerase 1 (EC 2.7.7.7) | protein | 755 | 42% helix, 23% strand | P0CL77 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains T, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1079 | 0.84 | 0.85 | 88 | MG, MES |
| 2 | 408 | 0.79 | 0.88 | 47 | empty |
| 3 | 60 | 0.49 | 0.86 | 14 | empty |
| 4 | 169 | 0.48 | 0.77 | 28 | empty |
| 5 | 87 | 0.48 | 0.82 | 18 | empty |
Interfaces
3 interfaces between chains.
- T–A · 1034 Ų buried · 24 hydrogen bonds · protein-nucleic
- P–A · 536 Ų buried · 16 hydrogen bonds · protein-nucleic
- T–P · 401 Ų buried · 37 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4FLY · 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 4FLY · PDBe 4FLY · UniProt P0CL77
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