MolNFT v1 · #162321 · protein
Crystal structure of the PRI1 subunit of human primase bound to datp
6R5D · DNA primase small subunit: “Crystal structure of the PRI1 subunit of human primase bound to datp”. X-ray diffraction, 3 ligands (DTP, MN, ZN), 12 pockets (best druggability 0.76). MolNFT v1 #162321 on GenesisL1: 3D structure…
- PDB
- 6R5D
- Type
- protein
- Length
- 769 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
- P49642
- Ligands
- DTP, MN, ZN
- Pockets
- 12 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA primase small subunit (EC 2.7.7.-) | protein | 384 | 48% helix, 12% strand | P49642 |
| E | DNA primase small subunit (EC 2.7.7.-) | protein | 385 | 50% helix, 12% strand | P49642 |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 2 copies · chains A, E
- MN · Manganese (II) ion · metal · 4 copies · chains A, E
- ZN · Zinc ion · metal · 2 copies · chains A, E
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1146 | 0.76 | 0.78 | 96 | EDO |
| 2 | 112 | 0.48 | 0.80 | 15 | empty |
| 3 | 185 | 0.47 | 0.76 | 22 | MN, DTP |
| 4 | 174 | 0.45 | 0.75 | 28 | MN, DTP |
| 5 | 77 | 0.44 | 0.81 | 14 | EDO |
Interfaces
1 interface between chains.
- A–E · 1005 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6R5D · Crystal structure of the Pri1 subunit of human primase bound to dATP · 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 E 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 6R5D · PDBe 6R5D · UniProt P49642
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