MolNFT v1 · #91724 · protein + DNA
Pyrococcus abyssi B family DNA polymerase bound to a dsdna, in edition mode
4FLU: “Pyrococcus abyssi B family DNA polymerase bound to a dsdna, in edition mode”. X-ray diffraction, 1 ligand (MG), 9 pockets (best druggability 0.84). MolNFT v1 #91724 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4FLU
- Type
- protein + DNA
- Length
- 782 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyrococcus abyssi B family DNA polymerase; Primer strand; Template strand
- EC
- 2.7.7.7
- UniProt
- P0CL77
- Ligands
- MG
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyrococcus abyssi B family DNA polymerase (EC 2.7.7.7) | protein | 758 | 41% helix, 22% strand | P0CL77 |
| P | Primer strand | dna | 11 | — | — |
| T | Template strand | dna | 13 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, P
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A, T
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 659 | 0.84 | 0.88 | 75 | MG, MES, GOL |
| 2 | 470 | 0.79 | 0.87 | 49 | empty |
| 3 | 669 | 0.67 | 0.76 | 65 | empty |
| 4 | 177 | 0.52 | 0.78 | 18 | empty |
| 5 | 51 | 0.45 | 0.85 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1214 Ų buried · 33 hydrogen bonds · protein-nucleic
- A–P · 1129 Ų buried · 41 hydrogen bonds · protein-nucleic
- P–T · 406 Ų buried · 43 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4FLU · Pyrococcus abyssi B family DNA polymerase bound to a dsDNA, in edition mode · the same entry in another collection · chain A against A, 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 4FLU · PDBe 4FLU · UniProt P0CL77
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