Research workbench
Crystal structure of the intein homing endonuclease pi-scei bound to its recognition sequence
Analyse Crystal structure of the intein homing endonuclease pi-scei bound to its… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LWS
- Type
- protein + DNA
- Length
- 495 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pi-scei DNA recognition region top strand; Pi-scei DNA recognition region bottom strand…
- EC
- 3.1.-.-
- UniProt
- P17255
- Ligands
- CA
- Pockets
- 12 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 24% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Pi-scei DNA recognition region top strand | dna | 34 | — | — |
| C | Pi-scei DNA recognition region bottom strand | dna | 34 | — | — |
| A | Endonuclease pi-scei (EC 3.1.-.-) | protein | 427 | 24% helix, 32% strand | P17255 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 761 | 0.72 | 0.78 | 77 | empty |
| 2 | 483 | 0.72 | 0.82 | 53 | CA |
| 3 | 135 | 0.64 | 0.87 | 25 | empty |
| 4 | 91 | 0.57 | 0.86 | 19 | empty |
| 5 | 131 | 0.53 | 0.82 | 16 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1519 Ų buried · 119 hydrogen bonds · nucleic-nucleic
- C–A · 1493 Ų buried · 28 hydrogen bonds · protein-nucleic
- B–A · 1389 Ų buried · 22 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 1LWS · Crystal structure of the intein homing endonuclease PI-SceI bound to its recognition… · the same entry in another collection · chain B against B, TM-score 1.00
- P17255 · AlphaFold monomer V2.0 prediction for V-type proton ATPase catalytic subunit a (P17255) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 P17255
- Elsewhere: RCSB PDB 1LWS · PDBe 1LWS · UniProt P17255
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