Research workbench
Structure of type iil restriction-modification enzyme mmei in complex with DNA has implications for engineering of new specificities
Analyse Structure of type iil restriction-modification enzyme mmei in complex with DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HR4
- Type
- protein + DNA
- Length
- 1,551 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mmei; DNA (5'-D(P*TP*AP*TP*CP*CP*GP*AP*CP*AP*TP*AP*AP*C)-3'); DNA…
- UniProt
- B2MU09
- Ligands
- SFG, CA
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 48% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Mmei | protein | 749 | 48% helix, 13% strand | B2MU09 |
| H, K | DNA (5'-D(P*TP*AP*TP*CP*CP*GP*AP*CP*AP*TP*AP*AP*C)-3') | dna | 13 | — | — |
| I | DNA (5'-D(P*GP*TP*TP*AP*TP*GP*TP*CP*GP*GP*AP*TP*A)-3') | dna | 13 | — | — |
| J | Mmei | protein | 751 | 48% helix, 13% strand | B2MU09 |
| L | DNA (5'-D(P*GP*TP*TP*AP*TP*GP*TP*CP*GP*GP*AP*TP*A)-3') | dna | 12 | — | — |
Ligands and binding sites
- SFG · Sinefungin · ligand · 2 copies · chains C, H, J, K
- CA · Calcium ion · metal · 2 copies · chains C, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 171 | 0.76 | 0.92 | 38 | SFG |
| 2 | 149 | 0.74 | 0.92 | 38 | SFG |
| 3 | 356 | 0.61 | 0.77 | 38 | empty |
| 4 | 323 | 0.59 | 0.77 | 38 | empty |
| 5 | 194 | 0.58 | 0.81 | 26 | empty |
Interfaces
7 interfaces between chains.
- J–K · 1279 Ų buried · 32 hydrogen bonds · protein-nucleic
- C–H · 1271 Ų buried · 30 hydrogen bonds · protein-nucleic
- J–L · 1136 Ų buried · 23 hydrogen bonds · protein-nucleic
- C–I · 1116 Ų buried · 21 hydrogen bonds · protein-nucleic
- C–J · 1010 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5HR4 · Structure of Type IIL restriction-modification enzyme MmeI in complex with DNA has… · the same entry in another collection · chain J against J, 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 B2MU09
- Elsewhere: RCSB PDB 5HR4 · PDBe 5HR4 · UniProt B2MU09
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