Research workbench
I-scei in complex with a top nicked DNA substrate
Analyse I-scei in complex with a top nicked DNA substrate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3C0X
- Type
- protein + DNA
- Length
- 271 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Intron-encoded endonuclease I-scei; DNA (5'- D(*DC*DAP*DCP*DGP*DCP*DTP*DAP*DGP*DGP*DGP*DAP…
- EC
- 3.1.-.-
- UniProt
- P03882
- Ligands
- CA
- Pockets
- 7 · best druggability 0.55
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Intron-encoded endonuclease I-scei (EC 3.1.-.-) | protein | 223 | 43% helix, 21% strand | P03882 |
| B | DNA (5'- D(*DC*DAP*DCP*DGP*DCP*DTP*DAP*DGP*DGP*DGP*DAP*DTP*DAP*DA)- 3') | dna | 13 | — | — |
| C | DNA (5'- D(P*DCP*DAP*DGP*DGP*DGP*DTP*DAP*DAP*DTP*DAP*DC)-3') | dna | 11 | — | — |
| D | DNA (5'- D(*DG*DGP*DTP*DAP*DTP*DTP*DAP*DCP*DCP*DCP*DTP*DGP*DTP*DTP*D AP*DTP*DCP*DCP*DCP*DTP*DAP*DGP*DCP*DGP*DT)-3') | dna | 24 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains B, C, D, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 63 | 0.55 | 0.89 | 21 | empty |
| 2 | 74 | 0.52 | 0.86 | 19 | empty |
| 3 | 116 | 0.47 | 0.80 | 21 | empty |
| 4 | 51 | 0.42 | 0.83 | 15 | empty |
| 5 | 108 | 0.42 | 0.77 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1271 Ų buried · 25 hydrogen bonds · protein-nucleic
- A–B · 737 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–D · 661 Ų buried · 55 hydrogen bonds · nucleic-nucleic
- A–C · 633 Ų buried · 14 hydrogen bonds · protein-nucleic
- C–D · 559 Ų buried · 47 hydrogen bonds · nucleic-nucleic
Compared structures
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 P03882
- Elsewhere: RCSB PDB 3C0X · PDBe 3C0X · UniProt P03882
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