MolNFT v1 · #118404 · protein + DNA + RNA
Crystal structure of C-terminal domain of the human DNA primase large subunit with bound DNA TEMPLATE/RNA primer and manganese ion
5F0S: “Crystal structure of C-terminal domain of the human DNA primase large subunit with bound DNA TEMPLATE/RNA…”. X-ray diffraction, 2 ligands (SF4, MN), 6 pockets (best druggability 0.73). MolNFT v1 #118404 on GenesisL1: 3D structure…
- PDB
- 5F0S
- Type
- protein + DNA + RNA
- Length
- 406 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA primase large subunit; RNA (5'-R(P*GP*GP*CP*GP*GP*C)-3'); DNA…
- EC
- 2.7.7.-
- UniProt
- P49643
- Ligands
- SF4, MN
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 64% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA primase large subunit (EC 2.7.7.-) | protein | 187 | 65% helix, 1% strand | P49643 |
| B | DNA primase large subunit (EC 2.7.7.-) | protein | 185 | 64% helix, 1% strand | P49643 |
| C, E | RNA (5'-R(P*GP*GP*CP*GP*GP*C)-3') | rna | 6 | — | — |
| D | DNA (5'-D(*GP*CP*CP*GP*CP*CP*AP*AP*CP*AP*TP*A)-3') | dna | 12 | — | — |
| F | DNA (5'-D(*GP*CP*CP*GP*CP*CP*AP*AP*CP*AP*TP*A)-3') | dna | 10 | — | — |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, C, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 599 | 0.73 | 0.80 | 45 | empty |
| 2 | 79 | 0.71 | 0.95 | 21 | empty |
| 3 | 294 | 0.66 | 0.82 | 29 | MN |
| 4 | 209 | 0.54 | 0.79 | 15 | MN |
| 5 | 122 | 0.50 | 0.80 | 16 | empty |
Interfaces
7 interfaces between chains.
- A–D · 915 Ų buried · 21 hydrogen bonds · protein-nucleic
- B–F · 736 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–B · 473 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 308 Ų buried · 31 hydrogen bonds · nucleic-nucleic
- E–F · 298 Ų buried · 27 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 5F0S · Crystal structure of C-terminal domain of the human DNA primase large subunit with bound… · the same entry in another collection · chain F against F, TM-score 1.00
- 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 0.99
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 P49643
- Elsewhere: RCSB PDB 5F0S · PDBe 5F0S · UniProt P49643
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