MolNFT v1 · #118299 · protein
Crystal structure of human primosome
5EXR · DNA primase small subunit: “Crystal structure of human primosome”. X-ray diffraction, 2 ligands (SF4, ZN), 20 pockets (best druggability 0.84). MolNFT v1 #118299 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5EXR
- Type
- protein
- Length
- 4,648 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA primase small subunit; DNA primase large subunit; DNA polymerase alpha catalytic…
- EC
- 2.7.7.-, 2.7.7.7
- UniProt
- P49642, P49643, P09884, Q14181
- Ligands
- SF4, ZN
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | DNA primase small subunit (EC 2.7.7.-) | protein | 389 | 44% helix, 12% strand | P49642 |
| B, F | DNA primase large subunit (EC 2.7.7.-) | protein | 434 | 56% helix, 3% strand | P49643 |
| C, G | DNA polymerase alpha catalytic subunit (EC 2.7.7.7) | protein | 1057 | 39% helix, 19% strand | P09884 |
| D, H | DNA polymerase alpha subunit B | protein | 444 | 21% helix, 25% strand | Q14181 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains B, F
- ZN · Zinc ion · metal · 6 copies · chains A, C, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 429 | 0.84 | 0.92 | 72 | empty |
| 2 | 386 | 0.84 | 0.92 | 68 | empty |
| 3 | 1186 | 0.83 | 0.84 | 122 | empty |
| 4 | 368 | 0.82 | 0.91 | 54 | empty |
| 5 | 642 | 0.78 | 0.83 | 79 | empty |
Interfaces
11 interfaces between chains.
- F–G · 2680 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 2604 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 2581 Ų buried · 27 hydrogen bonds · protein-protein
- G–H · 2498 Ų buried · 29 hydrogen bonds · protein-protein
- C–G · 1311 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5EXR · Crystal structure of human primosome · the same entry in another collection · chain H against H, 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 0.98
- Q14181 · AlphaFold monomer V2.0 prediction for DNA polymerase alpha subunit B (Q14181) · a predicted model of the same protein · chain D against A, TM-score 0.98
- 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 0.94
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
- Every structure of UniProt P09884
- Every structure of UniProt Q14181
- Elsewhere: RCSB PDB 5EXR · PDBe 5EXR · UniProt P49642 · UniProt P49643 · UniProt P09884 · UniProt Q14181
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