MolNFT v1 · #91731 · protein + DNA
Pyrococcus abyssi B family DNA polymerase bound to a dsdna, in edition mode
4FM1 · DNA polymerase 1: “Pyrococcus abyssi B family DNA polymerase bound to a dsdna, in edition mode”. X-ray diffraction, 1 ligand (MN), 11 pockets (best druggability 0.81). MolNFT v1 #91731 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4FM1
- Type
- protein + DNA
- Length
- 776 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase 1; Primer strand; Template strand
- EC
- 2.7.7.7
- UniProt
- P0CL77
- Ligands
- MN
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase 1 (EC 2.7.7.7) | protein | 755 | 41% helix, 23% strand | P0CL77 |
| P | Primer strand | dna | 8 | — | — |
| T | Template strand | dna | 13 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A
- GOL · Glycerol · additive · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 797 | 0.81 | 0.84 | 70 | GOL, MES, MN |
| 2 | 520 | 0.78 | 0.85 | 48 | empty |
| 3 | 521 | 0.72 | 0.81 | 38 | MN |
| 4 | 157 | 0.52 | 0.79 | 21 | empty |
| 5 | 115 | 0.48 | 0.80 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1048 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–P · 538 Ų buried · 16 hydrogen bonds · protein-nucleic
- P–T · 399 Ų buried · 39 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4FM1 · 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 4FM1 · PDBe 4FM1 · UniProt P0CL77
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