Research workbench
Type II dehydroquinase from mycobacterium tuberculosis complexed with 3-dehydroshikimate
Analyse Type II dehydroquinase from mycobacterium tuberculosis complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3N59
- Type
- protein
- Length
- 3,286 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
- 3DS, CL
- Pockets
- 20 · best druggability 0.69
Structure
x-ray diffraction · 14 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 139 | 45% helix, 18% strand | P0A4Z6 |
| B, N | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 136 | 44% helix, 18% strand | P0A4Z6 |
| C | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 142 | 44% helix, 19% strand | P0A4Z6 |
| D | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 138 | 45% helix, 20% strand | P0A4Z6 |
| E | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 136 | 46% helix, 18% strand | P0A4Z6 |
| F, H, I, J, O, P, R, T, V, W | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 135 | 47% helix, 19% strand | P0A4Z6 |
| G | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 142 | 46% helix, 18% strand | P0A4Z6 |
| K | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 137 | 45% helix, 18% strand | P0A4Z6 |
| L | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 138 | 41% helix, 18% strand | P0A4Z6 |
| M | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 146 | 45% helix, 17% strand | P0A4Z6 |
| Q | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 138 | 44% helix, 18% strand | P0A4Z6 |
| S | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 136 | 42% helix, 18% strand | P0A4Z6 |
| U | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 135 | 45% helix, 19% strand | P0A4Z6 |
| X | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 137 | 45% helix, 18% strand | P0A4Z6 |
Ligands and binding sites
- 3DS · (4S,5R)-4,5-dihydroxy-3-oxocyclohex-1-ene-1-carboxylic acid · ligand · 2 copies · chains B, C, F, G
- CL · Chloride ion · ion · 24 copies · chains A, G, K, B, C, F, E, H, D, I, J, L, M, S, W, N, O, R, Q, T, P, U, V, 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 | 1072 | 0.69 | 0.74 | 90 | empty |
| 2 | 254 | 0.69 | 0.85 | 30 | empty |
| 3 | 50 | 0.69 | 0.98 | 27 | empty |
| 4 | 241 | 0.68 | 0.85 | 24 | empty |
| 5 | 54 | 0.68 | 0.97 | 28 | empty |
Interfaces
39 interfaces between chains.
- B–F · 1075 Ų buried · 19 hydrogen bonds · protein-protein
- O–T · 1050 Ų buried · 17 hydrogen bonds · protein-protein
- A–G · 1043 Ų buried · 16 hydrogen bonds · protein-protein
- N–R · 1040 Ų buried · 20 hydrogen bonds · protein-protein
- D–I · 1033 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 3N59 · Type II dehydroquinase from Mycobacterium Tuberculosis complexed with 3-dehydroshikimate · 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 3N59 · PDBe 3N59 · UniProt P0A4Z6
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