MolNFT v1 · #87070 · protein
Crystal structure of human primase bound to UTP
4BPW · DNA primase small subunit: “Crystal structure of human primase bound to UTP”. X-ray diffraction, 3 ligands (UTP, MG, ZN), 20 pockets (best druggability 0.60). MolNFT v1 #87070 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4BPW
- Type
- protein
- Length
- 1,176 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA primase small subunit; DNA primase large subunit
- EC
- 2.7.7.-
- UniProt
- P49642, P49643
- Ligands
- UTP, MG, ZN
- Pockets
- 20 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 56% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA primase small subunit (EC 2.7.7.-) | protein | 382 | 51% helix, 12% strand | P49642 |
| B | DNA primase large subunit (EC 2.7.7.-) | protein | 219 | 62% helix, 5% strand | P49643 |
| C | DNA primase small subunit (EC 2.7.7.-) | protein | 367 | 51% helix, 13% strand | P49642 |
| D | DNA primase large subunit (EC 2.7.7.-) | protein | 208 | 66% helix, 6% strand | P49643 |
Ligands and binding sites
- UTP · Uridine 5'-triphosphate · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · 4 copies · chains A, C
- 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 | 344 | 0.60 | 0.77 | 26 | empty |
| 2 | 233 | 0.49 | 0.74 | 24 | empty |
| 3 | 215 | 0.47 | 0.74 | 21 | empty |
| 4 | 98 | 0.47 | 0.80 | 15 | empty |
| 5 | 171 | 0.45 | 0.75 | 22 | MG, UTP |
Interfaces
5 interfaces between chains.
- A–B · 859 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 847 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 689 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 465 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 201 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4BPW · Crystal structure of human primase bound to UTP · the same entry in another collection · chain D against D, TM-score 1.00
- P49642 · AlphaFold monomer V2.0 prediction for DNA primase small subunit (P49642) · a predicted model of the same protein · chain C 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 0.96
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 P49643
- Elsewhere: RCSB PDB 4BPW · PDBe 4BPW · UniProt P49642 · UniProt P49643
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