Research workbench
Archaeal intron-encoded homing endonuclease I-VDI141I complexed with DNA
Analyse Archaeal intron-encoded homing endonuclease I-VDI141I complexed with DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3E54
- Type
- protein + DNA
- Length
- 362 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RRNA intron-encoded endonuclease; DNA (5'- D(*DCP*DTP*DGP*DAP*DCP*DTP*DCP*DTP*DCP*DTP*DTP*…
- EC
- 3.1.-.-
- UniProt
- Q6L703
- Ligands
- MG
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 5 distinct chains · 57% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RRNA intron-encoded endonuclease (EC 3.1.-.-) | protein | 159 | 57% helix, 18% strand | Q6L703 |
| C | DNA (5'- D(*DCP*DTP*DGP*DAP*DCP*DTP*DCP*DTP*DCP*DTP*DTP*DAP*DA)-3') | dna | 13 | — | — |
| D | DNA (5'-D(P*DGP*DGP*DTP*DAP*DGP*DCP*DCP*DAP*DA)-3') | dna | 9 | — | — |
| E | DNA (5'- D(*DTP*DTP*DGP*DGP*DCP*DTP*DAP*DCP*DCP*DTP*DTP*DAP*DA)-3') | dna | 13 | — | — |
| F | DNA (5'-D(P*DGP*DAP*DGP*DAP*DGP*DTP*DCP*DAP*DG)-3') | dna | 9 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 5 copies · chains A, B, D, E, C, F
- EOH · Ethanol · additive · 3 copies · chains B, D, E, C, A, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 85 | 0.70 | 0.94 | 21 | empty |
| 2 | 87 | 0.69 | 0.94 | 26 | empty |
| 3 | 114 | 0.52 | 0.82 | 19 | EOH |
| 4 | 95 | 0.46 | 0.80 | 20 | EOH |
Interfaces
14 interfaces between chains.
- A–B · 1126 Ų buried · 11 hydrogen bonds · protein-protein
- A–F · 897 Ų buried · 21 hydrogen bonds · protein-nucleic
- B–D · 887 Ų buried · 26 hydrogen bonds · protein-nucleic
- A–C · 879 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–E · 868 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
- 3E54 · Archaeal Intron-encoded Homing Endonuclease I-Vdi141I Complexed With DNA · 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 Q6L703
- Elsewhere: RCSB PDB 3E54 · PDBe 3E54 · UniProt Q6L703
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