Research workbench
Restriction endonuclease bamhi complex with DNA and calcium ions (pre- reactive complex).
Analyse Restriction endonuclease bamhi complex with DNA and calcium ions (pre- reactive… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BAM
- Type
- protein + DNA
- Length
- 440 residues
- Chains
- 4
- 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'); Protein (endonuclease bamhi)
- EC
- 3.1.21.4
- UniProt
- P23940
- Ligands
- CA
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 4 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*GP*GP*AP*TP*CP*CP*AP*TP*A)-3') | dna | 11 | — | — |
| A | Protein (endonuclease bamhi) (EC 3.1.21.4) | protein | 207 | 36% helix, 26% strand | P23940 |
| B | Protein (endonuclease bamhi) (EC 3.1.21.4) | protein | 210 | 39% helix, 26% strand | P23940 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains D, 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 479 | 0.75 | 0.84 | 32 | empty |
| 2 | 61 | 0.68 | 0.96 | 16 | empty |
| 3 | 115 | 0.58 | 0.86 | 19 | empty |
| 4 | 251 | 0.51 | 0.76 | 25 | empty |
| 5 | 87 | 0.44 | 0.80 | 16 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1245 Ų buried · 15 hydrogen bonds · protein-protein
- D–A · 891 Ų buried · 25 hydrogen bonds · protein-nucleic
- C–B · 677 Ų buried · 19 hydrogen bonds · protein-nucleic
- C–A · 637 Ų buried · 10 hydrogen bonds · protein-nucleic
- C–D · 536 Ų buried · 40 hydrogen bonds · nucleic-nucleic
Compared structures
- 2BAM · Restriction endonuclease bamhi complex with DNA and calcium ions (pre-reactive complex). · 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 B against A, TM-score 0.95
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 2BAM · PDBe 2BAM · UniProt P23940
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