Research workbench
Prim-pol domain of CRISPR-associated prim-pol (capp) from marinitoga sp. 1137 - primer initiation complex
Analyse Prim-pol domain of CRISPR-associated prim-pol (capp) from marinitoga sp. 1137… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7P9J
- Type
- protein + DNA
- Length
- 657 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TPR_REGION domain-containing protein; Templating strand
- UniProt
- H2J4R1
- Ligands
- DZ4, GTP, CO
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TPR_REGION domain-containing protein | protein | 218 | 33% helix, 28% strand | H2J4R1 |
| B | TPR_REGION domain-containing protein | protein | 218 | 33% helix, 27% strand | H2J4R1 |
| C | TPR_REGION domain-containing protein | protein | 215 | 34% helix, 28% strand | H2J4R1 |
| D | Templating strand | dna | 6 | — | — |
Ligands and binding sites
- DZ4 · 2'-deoxy-5'-O-[(R)-hydroxy{[(r)-hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]adenosine · ligand · 4 copies · chains A, B, D, C
- GTP · Guanosine-5'-triphosphate · ligand · chains B, D
- CO · Cobalt (II) ion · metal · 7 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 820 | 0.74 | 0.79 | 68 | empty |
| 2 | 534 | 0.68 | 0.78 | 51 | empty |
| 3 | 337 | 0.59 | 0.77 | 27 | CO, DZ4, GTP |
| 4 | 141 | 0.47 | 0.77 | 20 | CO, DZ4 |
| 5 | 109 | 0.39 | 0.76 | 18 | CO, DZ4 |
Interfaces
4 interfaces between chains.
- A–C · 566 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 476 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–C · 450 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 291 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7P9J · Prim-Pol Domain of CRISPR-associated Prim-Pol (CAPP) from Marinitoga sp. 1137 - Primer… · 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 7P9J · PDBe 7P9J · UniProt H2J4R1
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