Research workbench
Crystal structure of ubalai restriction endonuclease B3 domain domain (mutant L24M L53M L95M) with cognate DNA
Analyse Crystal structure of ubalai restriction endonuclease B3 domain domain (mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5O63
- Type
- protein + DNA
- Length
- 356 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Restriction endonuclease ubalai; DNA (5'-D(*C*G*C*C*A*G*G*G*C*)-3'); DNA…
- EC
- 3.1.21.4
- Pockets
- 1 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 19% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Restriction endonuclease ubalai (EC 3.1.21.4) | protein | 159 | 19% helix, 36% strand | — |
| B | Restriction endonuclease ubalai (EC 3.1.21.4) | protein | 161 | 19% helix, 36% strand | — |
| C, E | DNA (5'-D(*C*G*C*C*A*G*G*G*C*)-3') | dna | 9 | — | — |
| D, F | DNA (5'-D(*G*C*C*C*T*G*G*C*G*)-3') | dna | 9 | — | — |
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 397 | 0.60 | 0.76 | 57 | empty |
Interfaces
11 interfaces between chains.
- B–F · 516 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–D · 510 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–C · 509 Ų buried · 17 hydrogen bonds · protein-nucleic
- B–E · 508 Ų buried · 17 hydrogen bonds · protein-nucleic
- C–D · 439 Ų buried · 36 hydrogen bonds · nucleic-nucleic
Compared structures
- 5O63 · Crystal structure of UbaLAI restriction endonuclease B3 domain domain (mutant L24M L53M… · 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
- Elsewhere: RCSB PDB 5O63 · PDBe 5O63
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