Research workbench
ECOR124I-arda in the restriction-alleviation state
Analyse ECOR124I-arda 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
- 7BTR
- Type
- protein
- Length
- 2,087 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antirestriction protein arda; Type I restriction enzyme R protein; Type I restriction…
- EC
- 3.1.21.3, 2.1.1.72
- UniProt
- A0A0M2A928, Q304R3, P10484, P10485
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 5 distinct chains · 33% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, F | Antirestriction protein arda | protein | 163 | 37% helix, 14% strand | A0A0M2A928 |
| C | Type I restriction enzyme R protein (EC 3.1.21.3) | protein | 436 | 32% helix, 18% strand | Q304R3 |
| D | Type I restriction enzyme ECOR124II M protein (EC 2.1.1.72) | protein | 472 | 32% helix, 5% strand | P10484 |
| E | Type-1 restriction enzyme ECOR124II specificity protein | protein | 384 | 30% helix, 14% strand | P10485 |
| A | Type I restriction enzyme ECOR124II M protein (EC 2.1.1.72) | protein | 469 | 38% helix, 9% strand | P10484 |
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 | 999 | 0.84 | 0.85 | 92 | empty |
| 2 | 926 | 0.83 | 0.85 | 118 | empty |
| 3 | 1187 | 0.79 | 0.81 | 99 | empty |
| 4 | 1111 | 0.79 | 0.81 | 92 | empty |
| 5 | 198 | 0.78 | 0.93 | 37 | empty |
Interfaces
13 interfaces between chains.
- D–E · 1106 Ų buried · 2 hydrogen bonds · protein-protein
- E–A · 1105 Ų buried · 8 hydrogen bonds · protein-protein
- C–F · 711 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 598 Ų buried · 3 hydrogen bonds · protein-protein
- B–F · 568 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7BTR · EcoR124I-ArdA in the Restriction-Alleviation State · the same entry in another collection · chain A against A, 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 0.93
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 A0A0M2A928
- Every structure of UniProt Q304R3
- Every structure of UniProt P10484
- Every structure of UniProt P10485
- Elsewhere: RCSB PDB 7BTR · PDBe 7BTR · UniProt A0A0M2A928 · UniProt Q304R3 · UniProt P10484 · UniProt P10485
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