MolNFT v1 · #125170 · protein
Crystal structure of 2C-methyl-D-erythritol 2,4-clycodiphosphate synthase from burkholderia pseudomallei double mutant
5L12 · 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase: “Crystal structure of 2C-methyl-D-erythritol 2,4-clycodiphosphate synthase from burkholderia pseudomallei…”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability…
- PDB
- 5L12
- Type
- protein
- Length
- 459 residues
- Chains
- 3
- 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
- A3NWD9
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 31% 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 | 157 | 36% helix, 31% strand | A3NWD9 |
| B | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 154 | 34% helix, 31% strand | A3NWD9 |
| C | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 148 | 35% helix, 32% strand | A3NWD9 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 318 | 0.84 | 0.94 | 50 | empty |
| 2 | 239 | 0.57 | 0.79 | 36 | empty |
| 3 | 132 | 0.39 | 0.74 | 27 | empty |
| 4 | 103 | 0.34 | 0.73 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1089 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1076 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1063 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 5L12 · Crystal structure of 2C-methyl-D-erythritol 2,4-clycodiphosphate synthase from… · the same entry in another collection · chain A against A, TM-score 1.00
- A3NWD9 · AlphaFold monomer V2.0 prediction for 2-C-methyl-D-erythritol 2,4-cyclodiphosphate… · a predicted model of the same protein · chain C 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 A3NWD9
- Elsewhere: RCSB PDB 5L12 · PDBe 5L12 · UniProt A3NWD9
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