MolNFT v1 · #97275 · protein + DNA
Binary complex of 9N DNA polymerase in the replicative state
4K8X: “Binary complex of 9N DNA polymerase in the replicative state”. X-ray diffraction, 3 ligands (5CY, SO4, CL), 10 pockets (best druggability 0.78). MolNFT v1 #97275 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4K8X
- Type
- protein + DNA
- Length
- 787 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase; DNA (5'- D(P*AP*AP*AP*GP*GP*CP*GP*CP*AP*GP*TP*TP*CP*GP*CP*G)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q56366
- Ligands
- 5CY, SO4, CL
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase (EC 2.7.7.7) | protein | 759 | 42% helix, 23% strand | Q56366 |
| T | DNA (5'- D(P*AP*AP*AP*GP*GP*CP*GP*CP*AP*GP*TP*TP*CP*GP*CP*G)-3') | dna | 16 | — | — |
| P | DNA (5'-D(*CP*GP*CP*GP*AP*AP*CP*TP*GP*CP*GP*(DOC))-3') | dna | 12 | — | — |
Ligands and binding sites
- 5CY · 1-(3-hydroxypropyl)-2-{(1E,3E,5E)-5-[1-(3-hydroxypropyl)-3,3-dimethyl-1,3-dihydro-2H-indol-2-ylidene]penta-1,3-dien-1-yl}-3,3-dimethyl-3H-indolium · ligand · chains A, T
- SO4 · Sulfate ion · ion · 11 copies · chains A, T
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · chains A, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1159 | 0.78 | 0.80 | 71 | SO4 |
| 2 | 992 | 0.76 | 0.79 | 65 | SO4 |
| 3 | 160 | 0.70 | 0.90 | 30 | empty |
| 4 | 404 | 0.65 | 0.79 | 59 | SO4 |
| 5 | 198 | 0.54 | 0.78 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1381 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–P · 746 Ų buried · 24 hydrogen bonds · protein-nucleic
- T–P · 619 Ų buried · 66 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 disulfide, 1 covalent, 1 modified (disulfide, covalent ligand, nucleotide modification).
Compared structures
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 Q56366
- Elsewhere: RCSB PDB 4K8X · PDBe 4K8X · UniProt Q56366
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