MolNFT v1 · #91727 · protein + DNA
Pyrococcus abyssi B family DNA polymerase bound to a dsdna, in edition mode
4FLX · Template strand: “Pyrococcus abyssi B family DNA polymerase bound to a dsdna, in edition mode”. X-ray diffraction, 1 ligand (MG), 12 pockets (best druggability 0.83). MolNFT v1 #91727 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4FLX
- Type
- protein + DNA
- Length
- 779 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 0.83
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 22% 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 | 758 | 42% helix, 22% strand | P0CL77 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A
- GOL · Glycerol · additive · 2 copies · chains T, 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
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 544 | 0.83 | 0.89 | 64 | MG, MES, GOL |
| 2 | 433 | 0.79 | 0.87 | 48 | empty |
| 3 | 389 | 0.72 | 0.83 | 36 | MG |
| 4 | 159 | 0.55 | 0.80 | 18 | empty |
| 5 | 144 | 0.48 | 0.78 | 28 | empty |
Interfaces
3 interfaces between chains.
- T–A · 1169 Ų buried · 23 hydrogen bonds · protein-nucleic
- P–A · 551 Ų buried · 20 hydrogen bonds · protein-nucleic
- T–P · 399 Ų buried · 38 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4FLX · 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 4FLX · PDBe 4FLX · UniProt P0CL77
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