MolNFT v1 · #87071 · protein
Crystal structure of human primase in complex with the primase- binding motif of DNA polymerase alpha
4BPX · DNA primase small subunit: “Crystal structure of human primase in complex with the primase- binding motif of DNA polymerase alpha”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.56). MolNFT v1 #87071 on…
- PDB
- 4BPX
- Type
- protein
- Length
- 1,147 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA primase small subunit; DNA polymerase alpha catalytic subunit, DNA primase large…
- EC
- 2.7.7.-, 2.7.7.7
- UniProt
- P49642, P09884, P49643
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.56
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA primase small subunit (EC 2.7.7.-) | protein | 381 | 49% helix, 12% strand | P49642 |
| B | DNA polymerase alpha catalytic subunit, DNA primase large subunit (EC 2.7.7.7, 2.7.7.-) | protein | 181 | 67% helix, 7% strand | P09884, P49643 |
| C | DNA primase small subunit (EC 2.7.7.-) | protein | 372 | 48% helix, 12% strand | P49642 |
| D | DNA polymerase alpha catalytic subunit, DNA primase large subunit (EC 2.7.7.7, 2.7.7.-) | protein | 213 | 65% helix, 8% strand | P09884, P49643 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 151 | 0.56 | 0.81 | 23 | empty |
| 2 | 252 | 0.49 | 0.74 | 34 | empty |
| 3 | 186 | 0.46 | 0.75 | 22 | empty |
| 4 | 130 | 0.44 | 0.76 | 28 | empty |
| 5 | 110 | 0.44 | 0.78 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–B · 856 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 823 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 690 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 333 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 241 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4BPX · Crystal structure of human primase in complex with the primase- binding motif of DNA… · the same entry in another collection · chain A against A, TM-score 1.00
- P49642 · AlphaFold monomer V2.0 prediction for DNA primase small subunit (P49642) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P49643 · AlphaFold monomer V2.0 prediction for DNA primase large subunit (P49643) · a predicted model of the same protein · chain D against A, TM-score 0.92
- P09884 · AlphaFold monomer V2.0 prediction for DNA polymerase alpha catalytic subunit (P09884) · a predicted model of the same protein · chain D against A, TM-score 0.36
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 P49642
- Every structure of UniProt P09884
- Every structure of UniProt P49643
- Elsewhere: RCSB PDB 4BPX · PDBe 4BPX · UniProt P49642 · UniProt P09884 · UniProt P49643
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