MolNFT v1 · #106164 · protein
Crystal structure of human primase
4RR2 · DNA primase small subunit: “Crystal structure of human primase”. X-ray diffraction, 2 ligands (SF4, ZN), 20 pockets (best druggability 0.61). MolNFT v1 #106164 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4RR2
- Type
- protein
- Length
- 1,420 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
- SF4, ZN
- Pockets
- 20 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA primase small subunit (EC 2.7.7.-) | protein | 389 | 47% helix, 12% strand | P49642 |
| B | DNA primase large subunit (EC 2.7.7.-) | protein | 213 | 62% helix, 6% strand | P49643 |
| C | DNA primase small subunit (EC 2.7.7.-) | protein | 389 | 49% helix, 12% strand | P49642 |
| D | DNA primase large subunit (EC 2.7.7.-) | protein | 429 | 60% helix, 3% strand | P49643 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 81 | 0.61 | 0.89 | 19 | empty |
| 2 | 346 | 0.60 | 0.77 | 27 | empty |
| 3 | 131 | 0.51 | 0.79 | 21 | empty |
| 4 | 190 | 0.50 | 0.76 | 33 | empty |
| 5 | 144 | 0.49 | 0.78 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 834 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 832 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 407 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4RR2 · Crystal structure of human primase · the same entry in another collection · chain C against C, 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 B against A, TM-score 0.89
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 4RR2 · PDBe 4RR2 · UniProt P49642 · UniProt P49643
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