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Crystal structure of 3-dehydroquinate dehydratase from mycobacterium tuberculosis in complex with inhibitor 3
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
- 3N87
- Type
- protein
- Length
- 3,384 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
- N87
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 141 | 45% helix, 17% strand | P0A4Z6 |
Ligands and binding sites
- N87 · (1R,4R,5R)-1,4,5-trihydroxy-3-[3-(phenylcarbonyl)phenyl]cyclohex-2-ene-1-carboxylic 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
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 | 169 | 0.78 | 0.94 | 29 | N87 |
| 2 | 224 | 0.78 | 0.92 | 31 | N87 |
| 3 | 188 | 0.78 | 0.93 | 30 | N87 |
| 4 | 197 | 0.77 | 0.93 | 31 | N87 |
| 5 | 203 | 0.77 | 0.92 | 28 | N87 |
Interfaces
36 interfaces between chains.
- E–K · 1018 Ų buried · 14 hydrogen bonds · protein-protein
- P–U · 1005 Ų buried · 16 hydrogen bonds · protein-protein
- B–F · 1004 Ų buried · 15 hydrogen bonds · protein-protein
- V–X · 1003 Ų buried · 17 hydrogen bonds · protein-protein
- C–H · 996 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 3N87 · 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 3N87 · PDBe 3N87 · UniProt P0A4Z6
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