MolNFT v1 · #11449 · protein
Structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from haemophilus influenzae (HI0671)
1JN1: “Structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from haemophilus influenzae (HI0671)”. X-ray diffraction, 2 ligands (CO, SO4), 11 pockets (best druggability 0.85). MolNFT v1 #11449 on GenesisL1: 3D structure…
- PDB
- 1JN1
- Type
- protein
- Length
- 471 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
- UniProt
- P44815
- Ligands
- CO, SO4
- Pockets
- 11 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | protein | 157 | 36% helix, 25% strand | P44815 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 236 | 0.85 | 0.96 | 34 | SO4 |
| 2 | 102 | 0.68 | 0.92 | 23 | empty |
| 3 | 168 | 0.61 | 0.84 | 37 | empty |
| 4 | 67 | 0.60 | 0.91 | 23 | empty |
| 5 | 91 | 0.41 | 0.77 | 16 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1240 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1226 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1210 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 1JN1 · Structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Haemophilus… · the same entry in another collection · chain A against A, TM-score 1.00
- P44815 · AlphaFold monomer V2.0 prediction for 2-C-methyl-D-erythritol 2,4-cyclodiphosphate… · a predicted model of the same protein · chain A against A, TM-score 0.84
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 P44815
- Elsewhere: RCSB PDB 1JN1 · PDBe 1JN1 · UniProt P44815
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