MolNFT v1 · #103046 · protein
Crystal structure of mycobacterium tuberculosis shikimate dehydrogenase
4P4G · Shikimate 5-dehydrogenase aroe (5-dehydroshikimate…: “Crystal structure of mycobacterium tuberculosis shikimate dehydrogenase”. X-ray diffraction, 3 ligands (SKM, BR, SO4), 6 pockets (best druggability 0.76). MolNFT v1 #103046 on…
- PDB
- 4P4G
- Type
- protein
- Length
- 525 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Shikimate 5-dehydrogenase aroe (5-dehydroshikimate reductase)
- EC
- 1.1.1.25
- UniProt
- P95001
- Ligands
- SKM, BR, SO4
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Shikimate 5-dehydrogenase aroe (5-dehydroshikimate reductase) (EC 1.1.1.25) | protein | 265 | 44% helix, 22% strand | P95001 |
| B | Shikimate 5-dehydrogenase aroe (5-dehydroshikimate reductase) (EC 1.1.1.25) | protein | 260 | 45% helix, 21% strand | P95001 |
Ligands and binding sites
- SKM · (3R,4S,5R)-3,4,5-trihydroxycyclohex-1-ene-1-carboxylic acid · ligand · chains A
- BR · Bromide ion · ion · 7 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 558 | 0.76 | 0.83 | 71 | SKM, BR, SO4 |
| 2 | 275 | 0.68 | 0.84 | 29 | BR |
| 3 | 75 | 0.39 | 0.78 | 19 | empty |
| 4 | 67 | 0.35 | 0.77 | 16 | SO4 |
| 5 | 73 | 0.34 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 620 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4P4G · Crystal Structure of Mycobacterium tuberculosis Shikimate Dehydrogenase · the same entry in another collection · 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 P95001
- Elsewhere: RCSB PDB 4P4G · PDBe 4P4G · UniProt P95001
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