Research workbench
ECOR124I-DNA in the restriction-alleviation state
Analyse ECOR124I-DNA in the restriction-alleviation state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BTQ
- Type
- protein + DNA
- Length
- 2,412 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type I restriction enzyme ECOR124II M protein; DNA (64-mer); Type-1 restriction enzyme…
- EC
- 2.1.1.72, 3.1.21.3
- UniProt
- P10484, P10485, Q304R3
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 5 distinct chains · 39% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Type I restriction enzyme ECOR124II M protein (EC 2.1.1.72) | protein | 474 | 36% helix, 6% strand | P10484 |
| B | DNA (64-mer) | dna | 44 | — | — |
| C | DNA (64-mer) | dna | 44 | — | — |
| E | Type-1 restriction enzyme ECOR124II specificity protein | protein | 384 | 28% helix, 13% strand | P10485 |
| F | Type I restriction enzyme R protein (EC 3.1.21.3) | protein | 992 | 44% helix, 12% strand | Q304R3 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 955 | 0.83 | 0.84 | 115 | empty |
| 2 | 670 | 0.80 | 0.84 | 80 | empty |
| 3 | 984 | 0.79 | 0.81 | 123 | empty |
| 4 | 354 | 0.79 | 0.89 | 52 | empty |
| 5 | 124 | 0.77 | 0.95 | 33 | empty |
Interfaces
12 interfaces between chains.
- B–C · 1925 Ų buried · 179 hydrogen bonds · nucleic-nucleic
- D–E · 1491 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 1138 Ų buried · 2 hydrogen bonds · protein-protein
- A–F · 1129 Ų buried · 14 hydrogen bonds · protein-protein
- B–E · 891 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
- 7BTQ · EcoR124I-DNA in the Restriction-Alleviation State · the same entry in another collection · chain F against F, TM-score 1.00
- P10484 · AlphaFold monomer V2.0 prediction for type I restriction enzyme ECOR124II M protein… · a predicted model of the same protein · chain A against A, TM-score 0.94
- P10485 · AlphaFold monomer V2.0 prediction for type-1 restriction enzyme ECOR124II specificity… · a predicted model of the same protein · chain E against A, TM-score 0.88
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 P10484
- Every structure of UniProt P10485
- Every structure of UniProt Q304R3
- Elsewhere: RCSB PDB 7BTQ · PDBe 7BTQ · UniProt P10484 · UniProt P10485 · UniProt Q304R3
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