MolNFT v1 · #37351 · protein
Crystal structure of E. COLI enolase complexed with the minimal binding segment of RNase E.
2FYM: “Crystal structure of E. COLI enolase complexed with the minimal binding segment of RNase E.”. X-ray diffraction, 1 ligand (MG), 12 pockets (best druggability 0.77). MolNFT v1 #37351 on GenesisL1: 3D structure, binding sites and…
- 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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