Research workbench
Structure of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from mycobacterium tuberculosis in complex with an active site inhibitor
Analyse Structure of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PFP
- Type
- protein
- Length
- 928 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase arog
- EC
- 2.5.1.54
- UniProt
- O53512
- Ligands
- 035, 036, MN, CL, SO4
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Probable 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase arog (EC 2.5.1.54) | protein | 464 | 43% helix, 14% strand | O53512 |
Ligands and binding sites
- 035 · (2S)-2,7-bis(phosphonooxy)heptanoic acid · ligand · 2 copies · chains A, B
- 036 · (2R)-2,7-bis(phosphonooxy)heptanoic acid · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · chains B
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 909 | 0.80 | 0.82 | 104 | SO4 |
| 2 | 1027 | 0.77 | 0.79 | 95 | empty |
| 3 | 411 | 0.65 | 0.79 | 45 | empty |
| 4 | 128 | 0.57 | 0.84 | 24 | 035, 036 |
| 5 | 109 | 0.56 | 0.85 | 20 | 036, 035 |
Interfaces
1 interface between chains.
- A–B · 1992 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 3PFP · Structure of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Mycobacterium… · the same entry in another collection · chain A against A, TM-score 1.00
- O53512 · AlphaFold monomer V2.0 prediction for phospho-2-dehydro-3-deoxyheptonate aldolase arog… · a predicted model of the same protein · chain B 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 O53512
- Elsewhere: RCSB PDB 3PFP · PDBe 3PFP · UniProt O53512
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