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Structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from haemophilus influenzae (HI0671)

Analyse Structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 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

CO · Cobalt (II) ion · metal · 4 copies · chains A, B, C
SO4 · Sulfate ion · ion · chains A, B, C

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.

Pocket	Volume (Å³)	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 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 1226 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 1210 Å² 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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