Research workbench
Atomic model of the ocr-bound methylase complex from the type I restriction-modification enzyme ecoki (M2S1). based on fitting into EM MAP 1534.
Analyse Atomic model of the ocr-bound methylase complex from the type I… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y7C
- Type
- protein
- Length
- 1,734 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type-1 restriction enzyme ecoki specificity protein; Type I restriction enzyme ecoki M…
- EC
- 3.1.21.3, 2.1.1.72
- UniProt
- P05719, P08957, P03775
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 3 distinct chains · 46% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type-1 restriction enzyme ecoki specificity protein (EC 3.1.21.3) | protein | 464 | 44% helix, 15% strand | P05719 |
| B, C | Type I restriction enzyme ecoki M protein (EC 3.1.21.3, 2.1.1.72) | protein | 529 | 44% helix, 11% strand | P08957 |
| D, E | Gene 0.3 protein | protein | 106 | 67% helix, 0% strand | P03775 |
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 896 | 0.79 | 0.82 | 96 | empty |
| 2 | 839 | 0.78 | 0.81 | 86 | empty |
| 3 | 58 | 0.72 | 0.99 | 18 | empty |
| 4 | 617 | 0.72 | 0.79 | 67 | empty |
| 5 | 363 | 0.70 | 0.83 | 44 | empty |
Interfaces
10 interfaces between chains.
- C–E · 742 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 728 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 538 Ų buried · 0 hydrogen bonds · protein-protein
- A–E · 531 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 511 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2Y7C · Atomic model of the Ocr-bound methylase complex from the Type I restriction-modification… · the same entry in another collection · chain B against B, TM-score 1.00
- P08957 · AlphaFold monomer V2.0 prediction for type I restriction enzyme ecoki M protein (P08957) · a predicted model of the same protein · chain B against A, TM-score 0.83
- P05719 · AlphaFold monomer V2.0 prediction for type-1 restriction enzyme ecoki specificity protein… · a predicted model of the same protein · chain A against A, TM-score 0.69
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 P05719
- Every structure of UniProt P08957
- Every structure of UniProt P03775
- Elsewhere: RCSB PDB 2Y7C · PDBe 2Y7C · UniProt P05719 · UniProt P08957 · UniProt P03775
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