Research workbench
Crystal structure of type-II 3-dehydroquinase from C. albicans
Analyse Crystal structure of type-II 3-dehydroquinase from C. albicans in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KIP
- Type
- protein
- Length
- 3,456 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-dehydroquinase, type II
- EC
- 4.2.1.10
- UniProt
- Q59Z17
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, G, J, U, V | 3-dehydroquinase, type II (EC 4.2.1.10) | protein | 143 | 45% helix, 18% strand | Q59Z17 |
| D, T | 3-dehydroquinase, type II (EC 4.2.1.10) | protein | 144 | 42% helix, 18% strand | Q59Z17 |
| E, F, W, X | 3-dehydroquinase, type II (EC 4.2.1.10) | protein | 145 | 43% helix, 19% strand | Q59Z17 |
| H, K, L, M, N, O, P, Q, R, S | 3-dehydroquinase, type II (EC 4.2.1.10) | protein | 144 | 44% helix, 18% strand | Q59Z17 |
| I | 3-dehydroquinase, type II (EC 4.2.1.10) | protein | 147 | 46% helix, 18% strand | Q59Z17 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 24 copies · chains A, B, M, N, C, D, E, F, G, H, I, J, K, O, P, Q, R, S, T, U, V, W, X
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 8 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, 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 | 1106 | 0.85 | 0.85 | 86 | SO4 |
| 2 | 645 | 0.72 | 0.79 | 107 | TRS |
| 3 | 549 | 0.70 | 0.79 | 86 | TRS |
| 4 | 606 | 0.69 | 0.78 | 64 | SO4 |
| 5 | 352 | 0.68 | 0.82 | 26 | SO4 |
Interfaces
42 interfaces between chains.
- O–X · 807 Ų buried · 12 hydrogen bonds · protein-protein
- B–E · 805 Ų buried · 14 hydrogen bonds · protein-protein
- A–G · 797 Ų buried · 14 hydrogen bonds · protein-protein
- D–J · 797 Ų buried · 12 hydrogen bonds · protein-protein
- M–S · 795 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3KIP · Crystal structure of type-II 3-dehydroquinase from C. albicans · the same entry in another collection · chain K against K, 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 Q59Z17
- Elsewhere: RCSB PDB 3KIP · PDBe 3KIP · UniProt Q59Z17
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