MolNFT v1 · #72440 · protein
Crystal structure of 3-dehydroquinate dehydratase from mycobacterium tuberculosis in complex with inhibitor 6
3N8N: “Crystal structure of 3-dehydroquinate dehydratase from mycobacterium tuberculosis in complex with inhibitor 6”. X-ray diffraction, 1 ligand (N88), 20 pockets (best druggability 0.76). MolNFT v1 #72440 on GenesisL1: 3D structure…
- PDB
- 3N8N
- Type
- protein
- Length
- 3,325 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
- N88
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 13 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 137 | 45% helix, 18% strand | P0A4Z6 |
| C, H | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 136 | 47% helix, 18% strand | P0A4Z6 |
| D | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 141 | 45% helix, 19% strand | P0A4Z6 |
| E, I, O, Q, R, S, T, U, V, W | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 141 | 46% helix, 18% strand | P0A4Z6 |
| F | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 139 | 47% helix, 17% strand | P0A4Z6 |
| G | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 134 | 45% helix, 19% strand | P0A4Z6 |
| J | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 135 | 49% helix, 18% strand | P0A4Z6 |
| K | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 135 | 44% helix, 19% strand | P0A4Z6 |
| L | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 134 | 46% helix, 19% strand | P0A4Z6 |
| M | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 135 | 45% helix, 19% strand | P0A4Z6 |
| N | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 132 | 44% helix, 19% strand | P0A4Z6 |
| P | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 140 | 41% helix, 19% strand | P0A4Z6 |
| X | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 144 | 40% helix, 17% strand | P0A4Z6 |
Ligands and binding sites
- N88 · (1R,4R,5R)-3-(tert-butylcarbamoyl)-1,4,5-trihydroxycyclohex-2-ene-1-carboxylic acid · ligand · 14 copies · chains A, L, B, E, C, D, G, F, H, I, J, K, T, V, U
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 | 1079 | 0.76 | 0.79 | 101 | empty |
| 2 | 279 | 0.75 | 0.88 | 29 | N88 |
| 3 | 192 | 0.74 | 0.90 | 27 | N88 |
| 4 | 233 | 0.74 | 0.89 | 27 | empty |
| 5 | 170 | 0.73 | 0.91 | 29 | empty |
Interfaces
41 interfaces between chains.
- D–I · 1029 Ų buried · 17 hydrogen bonds · protein-protein
- V–X · 1018 Ų buried · 16 hydrogen bonds · protein-protein
- O–T · 1011 Ų buried · 19 hydrogen bonds · protein-protein
- J–L · 999 Ų buried · 17 hydrogen bonds · protein-protein
- P–U · 997 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 3N8N · 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 3N8N · PDBe 3N8N · UniProt P0A4Z6
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