Research workbench
ECOR124I-ocr in the intermediate state
Analyse ECOR124I-ocr in the intermediate state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BST
- Type
- protein
- Length
- 3,508 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type I restriction enzyme R protein; Type I restriction enzyme ECOR124II M protein…
- EC
- 3.1.21.3, 2.1.1.72
- UniProt
- Q304R3, P10484, P03775, P10485
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 6 distinct chains · 39% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Type I restriction enzyme R protein (EC 3.1.21.3) | protein | 975 | 43% helix, 11% strand | Q304R3 |
| C | Type I restriction enzyme R protein (EC 3.1.21.3) | protein | 992 | 43% helix, 11% strand | Q304R3 |
| D | Type I restriction enzyme ECOR124II M protein (EC 2.1.1.72) | protein | 472 | 32% helix, 7% strand | P10484 |
| E | Type I restriction enzyme ECOR124II M protein (EC 2.1.1.72) | protein | 473 | 33% helix, 6% strand | P10484 |
| F, G | Overcome classical restriction GP0.3 | protein | 106 | 64% helix, 0% strand | P03775 |
| A | Type-1 restriction enzyme ECOR124II specificity protein | protein | 384 | 28% helix, 14% strand | P10485 |
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 | 1128 | 0.87 | 0.88 | 161 | empty |
| 2 | 776 | 0.84 | 0.87 | 85 | empty |
| 3 | 201 | 0.80 | 0.94 | 36 | empty |
| 4 | 518 | 0.79 | 0.85 | 83 | empty |
| 5 | 1058 | 0.79 | 0.80 | 100 | empty |
Interfaces
15 interfaces between chains.
- B–D · 1835 Ų buried · 16 hydrogen bonds · protein-protein
- E–A · 1494 Ų buried · 13 hydrogen bonds · protein-protein
- D–A · 1402 Ų buried · 7 hydrogen bonds · protein-protein
- C–E · 1096 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 915 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7BST · EcoR124I-Ocr in the Intermediate 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 D 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 A 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 Q304R3
- Every structure of UniProt P10484
- Every structure of UniProt P03775
- Every structure of UniProt P10485
- Elsewhere: RCSB PDB 7BST · PDBe 7BST · UniProt Q304R3 · UniProt P10484 · UniProt P03775 · UniProt P10485
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