Research workbench
Heterodimeric structure of the core primase.
Analyse Heterodimeric structure of the core primase. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZT2
- Type
- protein
- Length
- 1,056 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
- Q97Z83, Q9UWW1
- Ligands
- ZN, SO4
- Pockets
- 13 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA primase small subunit (EC 2.7.7.-) | protein | 327 | 29% helix, 24% strand | Q97Z83 |
| C | DNA primase small subunit (EC 2.7.7.-) | protein | 320 | 27% helix, 27% strand | Q97Z83 |
| B | DNA primase large subunit (EC 2.7.7.-) | protein | 207 | 58% helix, 12% strand | Q9UWW1 |
| D | DNA primase large subunit (EC 2.7.7.-) | protein | 202 | 59% helix, 10% strand | Q9UWW1 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · 39 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 971 | 0.72 | 0.76 | 82 | SO4 |
| 2 | 456 | 0.64 | 0.77 | 53 | SO4 |
| 3 | 321 | 0.56 | 0.76 | 39 | empty |
| 4 | 148 | 0.45 | 0.76 | 19 | empty |
| 5 | 150 | 0.44 | 0.75 | 26 | empty |
Interfaces
5 interfaces between chains.
- A–B · 922 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 920 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 877 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 701 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 48 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1ZT2 · Heterodimeric structure of the core primase. · the same entry in another collection · chain D against D, TM-score 1.00
- Q9UWW1 · AlphaFold monomer V2.0 prediction for DNA primase large subunit pril (Q9UWW1) · a predicted model of the same protein · chain D against A, TM-score 0.98
- Q97Z83 · AlphaFold monomer V2.0 prediction for DNA primase small subunit pris (Q97Z83) · a predicted model of the same protein · chain C 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 Q97Z83
- Every structure of UniProt Q9UWW1
- Elsewhere: RCSB PDB 1ZT2 · PDBe 1ZT2 · UniProt Q97Z83 · UniProt Q9UWW1
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