MolNFT v1 · #103855 · protein
Structure of initiator
4PT7 · Replication initiator a family protein: “Structure of initiator”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.76). MolNFT v1 #103855 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4PT7
- Type
- protein
- Length
- 527 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Replication initiator a family protein
- UniProt
- R9YU73
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Replication initiator a family protein | protein | 131 | 47% helix, 12% strand | R9YU73 |
| C, D, B | Replication initiator a family protein | protein | 132 | 47% helix, 12% strand | R9YU73 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains A, C, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 793 | 0.76 | 0.80 | 63 | SO4 |
| 2 | 183 | 0.50 | 0.77 | 29 | SO4 |
| 3 | 150 | 0.48 | 0.77 | 30 | empty |
| 4 | 211 | 0.47 | 0.75 | 27 | empty |
| 5 | 183 | 0.44 | 0.74 | 29 | empty |
Interfaces
5 interfaces between chains.
- D–B · 2148 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 2125 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 318 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 309 Ų buried · 3 hydrogen bonds · protein-protein
- C–B · 101 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4PT7 · Structure of initiator · 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 R9YU73
- Elsewhere: RCSB PDB 4PT7 · PDBe 4PT7 · UniProt R9YU73
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