MolNFT v1 · #129344 · protein
Enolase in complex with RNase E
5OHG: “Enolase in complex with RNase E”. X-ray diffraction, 3 ligands (NA, MG, PO4), 10 pockets (best druggability 0.79). MolNFT v1 #129344 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5OHG
- Type
- protein
- Length
- 1,796 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Enolase; Ribonuclease E
- EC
- 4.2.1.11, 3.1.26.12
- UniProt
- P0A6P9, P21513
- Ligands
- NA, MG, PO4
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H, I | Enolase (EC 4.2.1.11) | protein | 431 | 42% helix, 19% strand | P0A6P9 |
| B | Enolase (EC 4.2.1.11) | protein | 432 | 42% helix, 19% strand | P0A6P9 |
| C | Ribonuclease E (EC 3.1.26.12) | protein | 36 | 22% helix, 0% strand | P21513 |
| J | Ribonuclease E (EC 3.1.26.12) | protein | 35 | 23% helix, 0% strand | P21513 |
Ligands and binding sites
- NA · Sodium ion · metal · 5 copies · chains A, B, H, I
- MG · Magnesium ion · metal · 4 copies · chains A, B, H, I
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 882 | 0.79 | 0.82 | 109 | empty |
| 2 | 84 | 0.76 | 0.98 | 27 | empty |
| 3 | 135 | 0.75 | 0.94 | 54 | empty |
| 4 | 197 | 0.63 | 0.83 | 33 | empty |
| 5 | 307 | 0.61 | 0.79 | 33 | empty |
Interfaces
9 interfaces between chains.
- H–I · 1895 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 1882 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 967 Ų buried · 8 hydrogen bonds · protein-protein
- H–J · 921 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 744 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5OHG · enolase in complex with RNase E · the same entry in another collection · chain J against J, TM-score 1.00
- P0A6P9 · AlphaFold monomer V2.0 prediction for enolase (P0A6P9) · a predicted model of the same protein · chain I against A, TM-score 1.00
- P21513 · AlphaFold monomer V2.0 prediction for ribonuclease E (P21513) · a predicted model of the same protein · chain C against A, TM-score 0.35
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 5OHG · PDBe 5OHG · UniProt P0A6P9 · UniProt P21513
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