Research workbench
Crystal structure of 3-dehydroquinate dehydratase from mycobacterium tuberculosis in complex with inhibitor 2
Analyse Crystal structure of 3-dehydroquinate dehydratase from mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3N7A
- Type
- protein
- Length
- 3,374 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-dehydroquinate dehydratase
- EC
- 4.2.1.10
- UniProt
- P0A4Z6
- Ligands
- FA1
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 141 | 48% helix, 18% strand | P0A4Z6 |
| C | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 139 | 42% helix, 18% strand | P0A4Z6 |
| F | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 137 | 46% helix, 18% strand | P0A4Z6 |
| X | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 137 | 47% helix, 18% strand | P0A4Z6 |
Ligands and binding sites
- FA1 · 2,3 -anhydro-quinic acid · ligand · 24 copies · chains A, L, B, E, C, D, G, F, H, J, I, K, M, X, N, Q, O, P, S, R, T, V, U, W
- GOL · Glycerol · additive · 13 copies · chains B, E, C, F, G, H, J, I, K, L, N, O, P, S, Q, T, V, U, W, X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 147 | 0.75 | 0.93 | 27 | FA1 |
| 2 | 148 | 0.74 | 0.92 | 30 | FA1 |
| 3 | 131 | 0.73 | 0.93 | 28 | GOL, FA1 |
| 4 | 127 | 0.73 | 0.93 | 28 | GOL, FA1 |
| 5 | 135 | 0.73 | 0.92 | 29 | GOL, FA1 |
Interfaces
37 interfaces between chains.
- P–U · 998 Ų buried · 14 hydrogen bonds · protein-protein
- M–S · 995 Ų buried · 14 hydrogen bonds · protein-protein
- D–I · 995 Ų buried · 15 hydrogen bonds · protein-protein
- B–F · 993 Ų buried · 14 hydrogen bonds · protein-protein
- E–K · 992 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3N7A · Crystal structure of 3-dehydroquinate dehydratase from Mycobacterium tuberculosis in… · 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 P0A4Z6
- Elsewhere: RCSB PDB 3N7A · PDBe 3N7A · UniProt P0A4Z6
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