MolNFT v1 · #77406 · protein
Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from francisella tularensis
3RE3: “Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from francisella tularensis”. X-ray diffraction, 4 ligands (POP, NA, PO4), 8 pockets (best druggability 0.83). MolNFT v1 #77406 on GenesisL1: 3D structure…
- PDB
- 3RE3
- Type
- protein
- Length
- 583 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
- EC
- 4.6.1.12
- UniProt
- Q5NFU1
- Ligands
- POP, NA, PO4, CL
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 148 | 36% helix, 30% strand | Q5NFU1 |
| B | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 144 | 36% helix, 31% strand | Q5NFU1 |
| C | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 147 | 36% helix, 33% strand | Q5NFU1 |
| D | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 144 | 34% helix, 31% strand | Q5NFU1 |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · 2 copies · chains A, B, C
- NA · Sodium ion · metal · 3 copies · chains A, B, D, C
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains A, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 201 | 0.83 | 0.96 | 31 | PO4, MPD |
| 2 | 283 | 0.54 | 0.76 | 42 | MPD |
| 3 | 244 | 0.52 | 0.76 | 41 | POP |
| 4 | 124 | 0.43 | 0.76 | 19 | empty |
| 5 | 116 | 0.42 | 0.76 | 22 | CL |
Interfaces
5 interfaces between chains.
- B–D · 1045 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1034 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1032 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 678 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 60 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 3RE3 · Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase from… · the same entry in another collection · chain D against D, TM-score 1.00
- Q5NFU1 · AlphaFold monomer V2.0 prediction for 2-C-methyl-D-erythritol 2,4-cyclodiphosphate… · a predicted model of the same protein · chain B against A, TM-score 0.89
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 Q5NFU1
- Elsewhere: RCSB PDB 3RE3 · PDBe 3RE3 · UniProt Q5NFU1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.