Research workbench
Ispc in complex with an N-methyl-substituted hydroxamic acid
Analyse Ispc in complex with an N-methyl-substituted hydroxamic acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3R0I
- Type
- protein
- Length
- 786 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1-deoxy-D-xylulose 5-phosphate reductoisomerase
- EC
- 1.1.1.267
- UniProt
- P45568
- Ligands
- C0K, MN
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 1-deoxy-D-xylulose 5-phosphate reductoisomerase (EC 1.1.1.267) | protein | 393 | 51% helix, 15% strand | P45568 |
| B | 1-deoxy-D-xylulose 5-phosphate reductoisomerase (EC 1.1.1.267) | protein | 393 | 51% helix, 15% strand | P45568 |
Ligands and binding sites
- C0K · {(1S)-1-(3,4-difluorophenyl)-4-[hydroxy(methyl)amino]-4-oxobutyl}phosphonic acid · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 230 | 0.76 | 0.91 | 36 | empty |
| 2 | 493 | 0.65 | 0.77 | 70 | MN, C0K |
| 3 | 409 | 0.62 | 0.77 | 51 | C0K |
| 4 | 50 | 0.39 | 0.81 | 17 | empty |
| 5 | 53 | 0.32 | 0.77 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1634 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 3R0I · IspC in complex with an N-methyl-substituted hydroxamic acid · the same entry in another collection · chain A against A, TM-score 1.00
- P45568 · AlphaFold monomer V2.0 prediction for 1-deoxy-D-xylulose 5-phosphate reductoisomerase… · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P45568
- Elsewhere: RCSB PDB 3R0I · PDBe 3R0I · UniProt P45568
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