Research workbench
Crystal structure of yeast primase catalytic subunit
Analyse Crystal structure of yeast primase catalytic subunit in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MM2
- Type
- protein
- Length
- 790 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA primase small subunit
- EC
- 2.7.7.-
- UniProt
- P10363
- Ligands
- CD
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA primase small subunit (EC 2.7.7.-) | protein | 396 | 52% helix, 12% strand | P10363 |
| B | DNA primase small subunit (EC 2.7.7.-) | protein | 394 | 52% helix, 12% strand | P10363 |
Ligands and binding sites
- CD · Cadmium ion · metal · 10 copies · chains A, B
- CIT · Citric acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 494 | 0.68 | 0.79 | 51 | empty |
| 2 | 140 | 0.44 | 0.76 | 21 | CD, CIT |
| 3 | 151 | 0.38 | 0.73 | 29 | empty |
| 4 | 88 | 0.38 | 0.77 | 16 | CD, CIT |
| 5 | 93 | 0.35 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 897 Ų buried · 15 hydrogen bonds · protein-protein
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 P10363
- Elsewhere: RCSB PDB 4MM2 · PDBe 4MM2 · UniProt P10363
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.