Research workbench
Crystal structure of E. COLI enolase complexed with the minimal binding segment of RNase E.
Analyse Crystal structure of E. COLI enolase complexed with the minimal binding segment… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FYM
- Type
- protein
- Length
- 1,746 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Enolase; Ribonuclease E
- EC
- 4.2.1.11, 3.1.4.-
- UniProt
- P0A6P9, P21513
- Ligands
- MG
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Enolase (EC 4.2.1.11) | protein | 431 | 42% helix, 18% strand | P0A6P9 |
| B, E | Ribonuclease E (EC 3.1.4.-) | protein | 15 | 33% helix, 0% strand | P21513 |
| C | Enolase (EC 4.2.1.11) | protein | 427 | 43% helix, 18% strand | P0A6P9 |
| D | Enolase (EC 4.2.1.11) | protein | 427 | 43% helix, 19% strand | P0A6P9 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 85 | 0.77 | 0.99 | 26 | empty |
| 2 | 92 | 0.76 | 0.98 | 27 | empty |
| 3 | 404 | 0.69 | 0.81 | 66 | empty |
| 4 | 424 | 0.69 | 0.81 | 60 | empty |
| 5 | 564 | 0.67 | 0.77 | 66 | empty |
Interfaces
6 interfaces between chains.
- D–F · 1785 Ų buried · 41 hydrogen bonds · protein-protein
- A–C · 1748 Ų buried · 36 hydrogen bonds · protein-protein
- D–E · 563 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 536 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 428 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2FYM · Crystal structure of E. coli enolase complexed with the minimal binding segment of RNase… · the same entry in another collection · chain F against F, TM-score 1.00
- P0A6P9 · AlphaFold monomer V2.0 prediction for enolase (P0A6P9) · a predicted model of the same protein · chain F against A, TM-score 0.99
- P21513 · AlphaFold monomer V2.0 prediction for ribonuclease E (P21513) · a predicted model of the same protein · chain B against A, TM-score 0.41
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 P0A6P9
- Every structure of UniProt P21513
- Elsewhere: RCSB PDB 2FYM · PDBe 2FYM · UniProt P0A6P9 · UniProt P21513
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