Research workbench
ECOR124I-arda in the translocation state
Analyse ECOR124I-arda in the translocation state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BTO
- Type
- protein
- Length
- 2,644 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type I restriction enzyme ECOR124II M protein; Antirestriction protein arda; Type I…
- EC
- 2.1.1.72, 3.1.21.3
- UniProt
- P10484, A0A0M2A928, Q304R3, P10485
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 5 distinct chains · 33% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Type I restriction enzyme ECOR124II M protein (EC 2.1.1.72) | protein | 469 | 33% helix, 8% strand | P10484 |
| D, E | Antirestriction protein arda | protein | 163 | 38% helix, 13% strand | A0A0M2A928 |
| F, G | Type I restriction enzyme R protein (EC 3.1.21.3) | protein | 436 | 31% helix, 19% strand | Q304R3 |
| I | Type-1 restriction enzyme ECOR124II specificity protein | protein | 384 | 29% helix, 15% strand | P10485 |
| C, H | Type I restriction enzyme R protein (EC 3.1.21.3) | protein | 62 | 52% helix, 0% 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 | 718 | 0.84 | 0.88 | 82 | empty |
| 2 | 879 | 0.82 | 0.84 | 108 | empty |
| 3 | 1018 | 0.76 | 0.78 | 64 | empty |
| 4 | 526 | 0.75 | 0.83 | 67 | empty |
| 5 | 991 | 0.75 | 0.77 | 68 | empty |
Interfaces
17 interfaces between chains.
- A–I · 1394 Ų buried · 12 hydrogen bonds · protein-protein
- B–I · 1373 Ų buried · 9 hydrogen bonds · protein-protein
- B–H · 907 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 877 Ų buried · 9 hydrogen bonds · protein-protein
- E–G · 750 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7BTO · EcoR124I-ArdA in the Translocation State · the same entry in another collection · chain H against H, 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 0.95
- P10485 · AlphaFold monomer V2.0 prediction for type-1 restriction enzyme ECOR124II specificity… · a predicted model of the same protein · chain I against A, TM-score 0.90
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 A0A0M2A928
- Every structure of UniProt Q304R3
- Every structure of UniProt P10485
- Elsewhere: RCSB PDB 7BTO · PDBe 7BTO · UniProt P10484 · UniProt A0A0M2A928 · UniProt Q304R3 · UniProt P10485
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