Research workbench
Restriction endonuclease bamhi bound to a non-specific DNA.
Analyse Restriction endonuclease bamhi bound to a non-specific DNA. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ESG
- Type
- protein + DNA
- Length
- 437 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*TP*GP*GP*AP*TP*TP*CP*A)-3'); DNA (5'-D(*TP*GP*AP*AP*TP*CP*CP*A)-3'); Type II…
- EC
- 3.1.21.4
- UniProt
- P23940
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | DNA (5'-D(*TP*GP*GP*AP*TP*TP*CP*A)-3') | dna | 8 | — | — |
| D | DNA (5'-D(*TP*GP*AP*AP*TP*CP*CP*A)-3') | dna | 8 | — | — |
| A | Type II restriction enzyme bamhi (EC 3.1.21.4) | protein | 209 | 39% helix, 22% strand | P23940 |
| B | Type II restriction enzyme bamhi (EC 3.1.21.4) | protein | 212 | 41% helix, 22% strand | P23940 |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1121 | 0.82 | 0.84 | 88 | empty |
| 2 | 128 | 0.52 | 0.81 | 19 | empty |
| 3 | 123 | 0.49 | 0.80 | 18 | empty |
| 4 | 89 | 0.45 | 0.80 | 18 | empty |
Interfaces
6 interfaces between chains.
- A–B · 995 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 359 Ų buried · 23 hydrogen bonds · nucleic-nucleic
- C–A · 286 Ų buried · 1 hydrogen bond · protein-nucleic
- D–B · 177 Ų buried · 0 hydrogen bonds · protein-nucleic
- D–A · 166 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 1ESG · Restriction endonuclease bamhi bound to a non-specific DNA. · the same entry in another collection · chain C against C, TM-score 1.00
- P23940 · AlphaFold monomer V2.0 prediction for type-2 restriction enzyme bamhi (P23940) · a predicted model of the same protein · chain A against A, TM-score 0.87
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 P23940
- Elsewhere: RCSB PDB 1ESG · PDBe 1ESG · UniProt P23940
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