MolNFT v1 · #183453 · protein + DNA
Prim-pol domain of CRISPR-associated prim-pol (capp) from marinitoga sp. 1137 with dsdna
7NQF · TPR_REGION domain-containing protein: “Prim-pol domain of CRISPR-associated prim-pol (capp) from marinitoga sp. 1137 with dsdna”. X-ray diffraction, 1 ligand (CO), 5 pockets (best druggability 0.62). MolNFT v1 #183453 on GenesisL1…
- PDB
- 7NQF
- Type
- protein + DNA
- Length
- 461 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TPR_REGION domain-containing protein; DNA(CGTGDG)
- UniProt
- H2J4R1
- Ligands
- CO
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TPR_REGION domain-containing protein | protein | 218 | 34% helix, 26% strand | H2J4R1 |
| B | TPR_REGION domain-containing protein | protein | 219 | 35% helix, 26% strand | H2J4R1 |
| C, D, E, F | DNA(CGTGDG) | dna | 6 | — | — |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 4 copies · chains A, D, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.62 | 0.86 | 13 | empty |
| 2 | 178 | 0.47 | 0.77 | 22 | empty |
| 3 | 178 | 0.44 | 0.75 | 18 | empty |
| 4 | 50 | 0.42 | 0.83 | 16 | empty |
| 5 | 66 | 0.33 | 0.77 | 14 | empty |
Interfaces
7 interfaces between chains.
- A–B · 700 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 393 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–F · 356 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–E · 334 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–D · 329 Ų buried · 4 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 7NQF · Prim-Pol Domain of CRISPR-associated Prim-Pol (CAPP) from Marinitoga sp. 1137 with dsDNA · the same entry in another collection · chain A against A, TM-score 1.00
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 H2J4R1
- Elsewhere: RCSB PDB 7NQF · PDBe 7NQF · UniProt H2J4R1
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