MolNFT v1 · #61796 · protein + DNA
Sgrai with cognate DNA and manganese bound
3DW9 · DNA (5'- D(*DGP*DAP*DGP*DTP*DCP*DCP*DAP*DCP*DCP*DGP*DGP*DTP*…: “Sgrai with cognate DNA and manganese bound”. X-ray diffraction, 1 ligand (MN), 3 pockets (best druggability 0.76). MolNFT v1 #61796 on GenesisL1: 3D structure, binding…
- PDB
- 3DW9
- Type
- protein + DNA
- Length
- 705 residues
- Chains
- 4
- 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
- MN
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, F | 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 | 335 | 49% helix, 11% strand | Q9F6L0 |
| B | Sgrair restriction enzyme (EC 3.1.21.4) | protein | 334 | 49% helix, 13% strand | Q9F6L0 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains F, A, E, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 763 | 0.76 | 0.81 | 85 | empty |
| 2 | 395 | 0.74 | 0.85 | 55 | empty |
| 3 | 506 | 0.61 | 0.75 | 47 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1366 Ų buried · 7 hydrogen bonds · protein-protein
- E–A · 891 Ų buried · 21 hydrogen bonds · protein-nucleic
- F–B · 875 Ų buried · 22 hydrogen bonds · protein-nucleic
- E–F · 794 Ų buried · 79 hydrogen bonds · nucleic-nucleic
- F–A · 754 Ų buried · 18 hydrogen bonds · protein-nucleic
Compared structures
- 3DW9 · SgrAI with cognate DNA and manganese 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 3DW9 · PDBe 3DW9 · UniProt Q9F6L0
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