MolNFT v1 · #65823 · protein
Crystal structure of E. COLI enolase bound to its cognate RNase E recognition domain
3H8A: “Crystal structure of E. COLI enolase bound to its cognate RNase E recognition domain”. X-ray diffraction, 1 ligand (MG), 10 pockets (best druggability 0.80). MolNFT v1 #65823 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3H8A
- Type
- protein
- Length
- 1,774 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Enolase; RNase E
- EC
- 4.2.1.11
- UniProt
- P0A6P9
- Ligands
- MG
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Enolase (EC 4.2.1.11) | protein | 430 | 43% helix, 19% strand | P0A6P9 |
| D | Enolase (EC 4.2.1.11) | protein | 431 | 43% helix, 19% strand | P0A6P9 |
| E | RNase E | protein | 28 | 29% helix, 0% strand | — |
| F | RNase E | protein | 25 | 32% helix, 0% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 123 | 0.80 | 0.98 | 42 | empty |
| 2 | 853 | 0.79 | 0.81 | 100 | empty |
| 3 | 94 | 0.78 | 0.99 | 27 | empty |
| 4 | 520 | 0.76 | 0.84 | 71 | empty |
| 5 | 65 | 0.70 | 0.96 | 24 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1762 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 1734 Ų buried · 38 hydrogen bonds · protein-protein
- B–E · 776 Ų buried · 4 hydrogen bonds · protein-protein
- A–E · 681 Ų buried · 7 hydrogen bonds · protein-protein
- D–F · 676 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3H8A · Crystal structure of E. coli enolase bound to its cognate RNase E recognition domain · 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 D against A, TM-score 0.99
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
- Elsewhere: RCSB PDB 3H8A · PDBe 3H8A · UniProt P0A6P9
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