MolNFT v1 · #61777 · protein + DNA
Sgrai with cognate DNA and calcium bound
3DVO · DNA (5'- D(*DGP*DAP*DGP*DTP*DCP*DCP*DAP*DCP*DCP*DGP*DGP*DTP*…: “Sgrai with cognate DNA and calcium bound”. X-ray diffraction, 1 ligand (CA), 14 pockets (best druggability 0.78). MolNFT v1 #61777 on GenesisL1: 3D structure, binding…
- PDB
- 3DVO
- Type
- protein + DNA
- Length
- 1,412 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*DGP*DAP*DGP*DTP*DCP*DCP*DAP*DCP*DCP*DGP*DGP*DTP*DGP*DGP*DAP*DCP*DT P*DC)-3')…
- EC
- 3.1.21.4
- UniProt
- Q9F6L0
- Ligands
- CA
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, F, G, H | DNA (5'- D(*DGP*DAP*DGP*DTP*DCP*DCP*DAP*DCP*DCP*DGP*DGP*DTP*DGP*DGP*DAP*DCP*DT P*DC)-3') | dna | 18 | — | — |
| A | Sgrair restriction enzyme (EC 3.1.21.4) | protein | 334 | 51% helix, 11% strand | Q9F6L0 |
| B, D | Sgrair restriction enzyme (EC 3.1.21.4) | protein | 336 | 51% helix, 13% strand | Q9F6L0 |
| C | Sgrair restriction enzyme (EC 3.1.21.4) | protein | 334 | 49% helix, 13% strand | Q9F6L0 |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains F, A, E, B, H, C, G, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 366 | 0.78 | 0.88 | 58 | CA |
| 2 | 457 | 0.75 | 0.85 | 65 | CA |
| 3 | 402 | 0.75 | 0.85 | 55 | CA |
| 4 | 437 | 0.74 | 0.84 | 68 | empty |
| 5 | 442 | 0.64 | 0.78 | 41 | empty |
Interfaces
14 interfaces between chains.
- C–D · 1352 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1345 Ų buried · 8 hydrogen bonds · protein-protein
- F–B · 869 Ų buried · 18 hydrogen bonds · protein-nucleic
- E–A · 866 Ų buried · 21 hydrogen bonds · protein-nucleic
- H–D · 859 Ų buried · 22 hydrogen bonds · protein-nucleic
Compared structures
- 3DVO · SgrAI with cognate DNA and calcium bound · the same entry in another collection · chain E against E, 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 Q9F6L0
- Elsewhere: RCSB PDB 3DVO · PDBe 3DVO · UniProt Q9F6L0
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