MolNFT v1 · #8551 · protein
Structures of mecp synthase in complex with (I) cmp and (II) cmp and product
1H47 · 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase: “Structures of mecp synthase in complex with (I) cmp and (II) cmp and product”. X-ray diffraction, 3 ligands (C5P, GPP, ZN), 11 pockets (best druggability 0.86). MolNFT v1 #8551…
- 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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