MolNFT v1 · #125455 · protein
Crystal structure of human carbonic anhydrase II in complex with a quinoline oligoamide foldamer
5L9E · Carbonic anhydrase 2: “Crystal structure of human carbonic anhydrase II in complex with a quinoline oligoamide foldamer”. X-ray diffraction, 4 ligands (QUJ, QVE, 6H0), 10 pockets (best druggability 0.77). MolNFT v1 #125455 on…
- PDB
- 5L9E
- Type
- protein
- Length
- 1,031 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carbonic anhydrase 2
- EC
- 4.2.1.1
- UniProt
- P00918
- Ligands
- QUJ, QVE, 6H0, ZN
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Carbonic anhydrase 2 (EC 4.2.1.1) | protein | 259 | 16% helix, 29% strand | P00918 |
| C | Carbonic anhydrase 2 (EC 4.2.1.1) | protein | 257 | 16% helix, 30% strand | P00918 |
| D | Carbonic anhydrase 2 (EC 4.2.1.1) | protein | 256 | 16% helix, 30% strand | P00918 |
Ligands and binding sites
- QUJ · 8-azanyl-4-(2-methylpropoxy)quinoline-2-carboxylic acid · ligand · 8 copies
- QVE · 8-azanyl-4-(2-hydroxy-2-oxoethyloxy)quinoline-2-carboxylic acid · ligand · 8 copies
- 6H0 · ~{N}-[[3-(4-formamidobutoxy)phenyl]methyl]-4-sulfamoyl-benzamide · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 27 copies · chains A, C, B, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 974 | 0.77 | 0.79 | 71 | ZN |
| 2 | 605 | 0.62 | 0.74 | 53 | empty |
| 3 | 193 | 0.59 | 0.81 | 28 | 6H0, GOL |
| 4 | 194 | 0.59 | 0.81 | 28 | 6H0, GOL |
| 5 | 189 | 0.57 | 0.80 | 27 | 6H0, GOL |
Interfaces
4 interfaces between chains.
- A–B · 466 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 162 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 83 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 57 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5L9E · Crystal structure of human carbonic anhydrase II in complex with a quinoline oligoamide… · the same entry in another collection · chain D against D, TM-score 1.00
- P00918 · AlphaFold monomer V2.0 prediction for carbonic anhydrase 2 (P00918) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 P00918
- Elsewhere: RCSB PDB 5L9E · PDBe 5L9E · UniProt P00918
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