Research workbench
Restriction endonuclease bamhi complex with DNA and manganese ions (post-reactive complex)
Analyse Restriction endonuclease bamhi complex with DNA and manganese ions… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BAM
- Type
- protein + DNA
- Length
- 438 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*TP*AP*TP*GP*GP*AP*TP*CP*CP*AP*TP*A)- 3'); DNA (5'-D(*TP*AP*TP*G)-3'); DNA…
- EC
- 3.1.21.4
- UniProt
- P23940
- Ligands
- MN
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | DNA (5'-D(*TP*AP*TP*GP*GP*AP*TP*CP*CP*AP*TP*A)- 3') | dna | 12 | — | — |
| D | DNA (5'-D(*TP*AP*TP*G)-3') | dna | 4 | — | — |
| E | DNA (5'-D(P*GP*AP*TP*CP*CP*AP*TP*A)-3') | dna | 7 | — | — |
| A | Protein (restriction endonuclease bamhi) (EC 3.1.21.4) | protein | 206 | 36% helix, 27% strand | P23940 |
| B | Protein (restriction endonuclease bamhi) (EC 3.1.21.4) | protein | 209 | 38% helix, 26% strand | P23940 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains D, E, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 424 | 0.71 | 0.82 | 38 | empty |
| 2 | 103 | 0.63 | 0.89 | 17 | empty |
| 3 | 288 | 0.54 | 0.76 | 26 | MN |
| 4 | 122 | 0.42 | 0.77 | 20 | empty |
| 5 | 87 | 0.39 | 0.77 | 16 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1196 Ų buried · 17 hydrogen bonds · protein-protein
- E–A · 723 Ų buried · 19 hydrogen bonds · protein-nucleic
- C–B · 670 Ų buried · 20 hydrogen bonds · protein-nucleic
- C–A · 624 Ų buried · 12 hydrogen bonds · protein-nucleic
- C–E · 321 Ų buried · 25 hydrogen bonds · nucleic-nucleic
Compared structures
- 3BAM · Restriction endonuclease bamhi complex with DNA and manganese ions (post-reactive complex) · the same entry in another collection · chain D against D, 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 B against A, TM-score 0.94
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 3BAM · PDBe 3BAM · UniProt P23940
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