Research workbench
ECOR124I-ocr in restriction-alleviation state
Analyse ECOR124I-ocr in 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
- 7BTP
- Type
- protein
- Length
- 2,534 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type-1 restriction enzyme ECOR124II specificity protein; Type I restriction enzyme R…
- EC
- 3.1.21.3, 2.1.1.72
- UniProt
- P10485, Q304R3, P10484, P03775
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 4 distinct chains · 40% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Type-1 restriction enzyme ECOR124II specificity protein | protein | 384 | 26% helix, 15% strand | P10485 |
| A | Type I restriction enzyme R protein (EC 3.1.21.3) | protein | 992 | 44% helix, 12% strand | Q304R3 |
| B, C | Type I restriction enzyme ECOR124II M protein (EC 2.1.1.72) | protein | 473 | 37% helix, 9% strand | P10484 |
| D, F | Overcome classical restriction GP0.3 | protein | 106 | 65% helix, 0% strand | P03775 |
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 | 1011 | 0.88 | 0.89 | 139 | empty |
| 2 | 1131 | 0.85 | 0.86 | 128 | empty |
| 3 | 203 | 0.79 | 0.93 | 33 | empty |
| 4 | 1139 | 0.78 | 0.80 | 120 | empty |
| 5 | 1035 | 0.78 | 0.79 | 85 | empty |
Interfaces
13 interfaces between chains.
- E–B · 1322 Ų buried · 2 hydrogen bonds · protein-protein
- E–C · 1230 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 1186 Ų buried · 17 hydrogen bonds · protein-protein
- B–F · 810 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 793 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7BTP · EcoR124I-Ocr in 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 B 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 0.89
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 P10485
- Every structure of UniProt Q304R3
- Every structure of UniProt P10484
- Every structure of UniProt P03775
- Elsewhere: RCSB PDB 7BTP · PDBe 7BTP · UniProt P10485 · UniProt Q304R3 · UniProt P10484 · UniProt P03775
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