Research workbench
Crystal structure of the catalytic subunit of human primase bound to UTP and mn
Analyse Crystal structure of the catalytic subunit of human primase bound to UTP and mn in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LIL
- Type
- protein
- Length
- 370 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA primase small subunit
- EC
- 2.7.7.-
- UniProt
- P49642
- Ligands
- UTP, MN, ZN
- Pockets
- 6 · best druggability 0.40
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA primase small subunit (EC 2.7.7.-) | protein | 370 | 50% helix, 12% strand | P49642 |
Ligands and binding sites
- UTP · Uridine 5'-triphosphate · ligand · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains A
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 89 | 0.40 | 0.77 | 15 | empty |
| 2 | 99 | 0.37 | 0.75 | 20 | empty |
| 3 | 84 | 0.34 | 0.75 | 17 | MN, UTP |
| 4 | 54 | 0.31 | 0.76 | 11 | empty |
| 5 | 53 | 0.27 | 0.74 | 13 | empty |
Compared structures
- 4LIL · Crystal structure of the catalytic subunit of human primase bound to UTP and Mn · 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 0.97
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
- Elsewhere: RCSB PDB 4LIL · PDBe 4LIL · UniProt P49642
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