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Structures of mecp synthase in complex with (I) cmp and (II) cmp and product
Analyse Structures of mecp synthase in complex with (I) cmp and (II) cmp and product in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1H47
- Type
- protein
- Length
- 944 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase
- EC
- 4.6.1.12
- UniProt
- P62617
- Ligands
- C5P, GPP, ZN
- Pockets
- 11 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, F | 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 157 | 35% helix, 31% strand | P62617 |
| B, E | 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 158 | 34% helix, 30% strand | P62617 |
Ligands and binding sites
- C5P · Cytidine-5'-monophosphate · ligand · 6 copies · chains A, C, B, D, F, E
- GPP · Geranyl diphosphate · ligand · 2 copies · chains A, B, C, D, E, F
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 254 | 0.86 | 0.97 | 33 | GPP |
| 2 | 240 | 0.86 | 0.97 | 33 | GPP |
| 3 | 532 | 0.65 | 0.76 | 70 | empty |
| 4 | 326 | 0.63 | 0.79 | 35 | C5P |
| 5 | 369 | 0.62 | 0.78 | 38 | C5P |
Interfaces
12 interfaces between chains.
- A–B · 1072 Ų buried · 20 hydrogen bonds · protein-protein
- D–F · 1062 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 1052 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1027 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 1009 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1H47 · Structures of MECP synthase in complex with (i) CMP and (ii) CMP and product · the same entry in another collection · chain E against E, TM-score 1.00
- P62617 · 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 0.98
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 P62617
- Elsewhere: RCSB PDB 1H47 · PDBe 1H47 · UniProt P62617
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