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Crystal structure of a 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

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

PDB: 1VH8
Type: protein
Length: 913 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: P44815
Ligands: POP
Pockets: 14 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 33% helix, 36% 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	153	33% helix, 37% strand	P44815
B, C, D, E, F	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12)	protein	152	34% helix, 36% strand	P44815

Ligands and binding sites

POP · Pyrophosphate 2- · ligand · 2 copies · chains A, B, C, D, E, F
ACY · Acetic acid · additive · 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

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	246	0.85	0.97	31	POP, ACY
2	253	0.85	0.97	33	POP, ACY
3	528	0.63	0.76	56	empty
4	291	0.57	0.77	37	empty
5	272	0.56	0.77	29	empty

Interfaces

7 interfaces between chains.

D–E · 1161 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 1125 Å² buried · 19 hydrogen bonds · protein-protein
B–C · 1120 Å² buried · 17 hydrogen bonds · protein-protein
D–F · 1113 Å² buried · 20 hydrogen bonds · protein-protein
E–F · 1110 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 modified (engineered).

Compared structures

1VH8 · Crystal structure of a 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase · the same entry in another collection · chain F against F, 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 B against A, TM-score 0.85

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 1VH8 · PDBe 1VH8 · UniProt P44815

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