MolNFT v1 · #158288 · protein
Structure of E.COLI enolase in complex with an analog of the natural product sf-2312 metabolite.
6NPF: “Structure of E.COLI enolase in complex with an analog of the natural product sf-2312 metabolite.”. X-ray diffraction, 3 ligands (KVM, MG, SO4), 17 pockets (best druggability 0.83). MolNFT v1 #158288 on GenesisL1: 3D structure…
- PDB
- 6NPF
- Type
- protein
- Length
- 2,604 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Enolase
- EC
- 4.2.1.11
- UniProt
- B7MLA0
- Ligands
- KVM, MG, SO4
- Pockets
- 17 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Enolase (EC 4.2.1.11) | protein | 438 | 41% helix, 18% strand | B7MLA0 |
| B | Enolase (EC 4.2.1.11) | protein | 436 | 42% helix, 19% strand | B7MLA0 |
| D | Enolase (EC 4.2.1.11) | protein | 432 | 41% helix, 19% strand | B7MLA0 |
| F | Enolase (EC 4.2.1.11) | protein | 434 | 41% helix, 18% strand | B7MLA0 |
| E | Enolase (EC 4.2.1.11) | protein | 426 | 41% helix, 18% strand | B7MLA0 |
Ligands and binding sites
- KVM · [(3S)-1-hydroxy-2,5-dioxopyrrolidin-3-yl]phosphonic acid · ligand · 3 copies · chains D, F, E
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, F, E
- SO4 · Sulfate ion · ion · 11 copies · chains A, B, C, D, F, E
- GOL · Glycerol · additive · 4 copies · chains A, B, F, C, D, E
- TLA · L(+)-tartaric acid · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1188 | 0.83 | 0.84 | 107 | GOL, SO4 |
| 2 | 1025 | 0.83 | 0.84 | 105 | SO4, GOL |
| 3 | 841 | 0.80 | 0.83 | 67 | empty |
| 4 | 393 | 0.70 | 0.82 | 50 | TLA |
| 5 | 436 | 0.69 | 0.81 | 56 | KVM |
Interfaces
15 interfaces between chains.
- C–D · 1930 Ų buried · 45 hydrogen bonds · protein-protein
- A–B · 1880 Ų buried · 41 hydrogen bonds · protein-protein
- F–E · 1832 Ų buried · 43 hydrogen bonds · protein-protein
- D–E · 618 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 609 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6NPF · Structure of E.coli enolase in complex with an analog of the natural product SF-2312… · the same entry in another collection · chain E against E, TM-score 1.00
- B7MLA0 · AlphaFold monomer V2.0 prediction for enolase (B7MLA0) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 B7MLA0
- Elsewhere: RCSB PDB 6NPF · PDBe 6NPF · UniProt B7MLA0
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