MolNFT v1 · #122608 · protein + DNA
Human DNA polymerase alpha in binary complex with a DNA:DNA template- primer
5IUD · DNA polymerase alpha catalytic subunit: “Human DNA polymerase alpha in binary complex with a DNA:DNA template- primer”. X-ray diffraction, 20 pockets (best druggability 0.81). MolNFT v1 #122608 on GenesisL1: 3D structure, binding…
- PDB
- 5IUD
- Type
- protein + DNA
- Length
- 3,562 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase alpha catalytic subunit; DNA template; DNA primer
- EC
- 2.7.7.7
- UniProt
- P09884
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 9 distinct chains · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase alpha catalytic subunit (EC 2.7.7.7) | protein | 859 | 37% helix, 22% strand | P09884 |
| B, K | DNA template | dna | 15 | — | — |
| C, F, L | DNA primer | dna | 13 | — | — |
| D | DNA polymerase alpha catalytic subunit (EC 2.7.7.7) | protein | 871 | 37% helix, 22% strand | P09884 |
| E | DNA template | dna | 16 | — | — |
| G | DNA polymerase alpha catalytic subunit (EC 2.7.7.7) | protein | 863 | 37% helix, 22% strand | P09884 |
| H | DNA template | dna | 13 | — | — |
| I | DNA primer | dna | 10 | — | — |
| J | DNA polymerase alpha catalytic subunit (EC 2.7.7.7) | protein | 861 | 36% helix, 21% strand | P09884 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 971 | 0.81 | 0.82 | 102 | empty |
| 2 | 1040 | 0.80 | 0.81 | 102 | empty |
| 3 | 352 | 0.80 | 0.90 | 45 | empty |
| 4 | 463 | 0.79 | 0.87 | 52 | empty |
| 5 | 389 | 0.77 | 0.87 | 38 | empty |
Interfaces
17 interfaces between chains.
- A–D · 1539 Ų buried · 25 hydrogen bonds · protein-protein
- D–E · 1195 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–B · 1023 Ų buried · 19 hydrogen bonds · protein-nucleic
- J–K · 1010 Ų buried · 16 hydrogen bonds · protein-nucleic
- G–H · 959 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
- 5IUD · Human DNA polymerase alpha in binary complex with a DNA:DNA template-primer · the same entry in another collection · chain F against F, TM-score 1.00
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 P09884
- Elsewhere: RCSB PDB 5IUD · PDBe 5IUD · UniProt P09884
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