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Structure of 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase (bound form mg atoms)

Analyse Structure of 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase (bound form… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1IV3
Type: protein
Length: 900 residues
Chains: 6
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: Q8RQP5
Ligands: MG
Pockets: 9 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12)	protein	150	32% helix, 31% strand	Q8RQP5

Ligands and binding sites

MG · Magnesium ion · metal · 6 copies · chains A, C, B, D, F, E

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	179	0.77	0.93	36	empty
2	172	0.75	0.92	36	empty
3	875	0.72	0.77	73	empty
4	348	0.62	0.78	32	empty
5	344	0.59	0.77	34	empty

Interfaces

9 interfaces between chains.

D–E · 1002 Å² buried · 17 hydrogen bonds · protein-protein
E–F · 989 Å² buried · 20 hydrogen bonds · protein-protein
B–C · 989 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 986 Å² buried · 17 hydrogen bonds · protein-protein
D–F · 979 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

1IV3 · Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase (bound form MG atoms) · the same entry in another collection · chain C against C, TM-score 1.00
Q8RQP5 · 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 1.00

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 Q8RQP5
Elsewhere: RCSB PDB 1IV3 · PDBe 1IV3 · UniProt Q8RQP5

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