Research workbench
Crystal structure of 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (ispd) from burkholderia thailandensis complexed with CTP
Analyse Crystal structure of 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZDQ
- Type
- protein
- Length
- 898 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
- EC
- 2.7.7.60
- UniProt
- Q2SWT6
- Ligands
- CTP, CAD, MG
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (EC 2.7.7.60) | protein | 230 | 34% helix, 23% strand | Q2SWT6 |
| B, C | 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (EC 2.7.7.60) | protein | 224 | 35% helix, 24% strand | Q2SWT6 |
| D | 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (EC 2.7.7.60) | protein | 220 | 34% helix, 23% strand | Q2SWT6 |
Ligands and binding sites
- CTP · Cytidine-5'-triphosphate · ligand · 2 copies · chains A, D
- CAD · Cacodylic acid · ligand · chains C
- MG · Magnesium ion · metal · 2 copies · chains A
- ACT · Acetate ion · additive · 10 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 298 | 0.78 | 0.89 | 40 | ACT |
| 2 | 563 | 0.76 | 0.83 | 63 | ACT, CTP |
| 3 | 574 | 0.71 | 0.79 | 65 | empty |
| 4 | 285 | 0.62 | 0.80 | 43 | CTP, MG, ACT |
| 5 | 184 | 0.51 | 0.78 | 26 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2084 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 1921 Ų buried · 43 hydrogen bonds · protein-protein
- B–D · 382 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 65 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4ZDQ · Crystal Structure of 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD) from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q2SWT6 · AlphaFold monomer V2.0 prediction for 2-C-methyl-D-erythritol 4-phosphate… · 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 Q2SWT6
- Elsewhere: RCSB PDB 4ZDQ · PDBe 4ZDQ · UniProt Q2SWT6
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