MolNFT v1 · #30744 · protein
Haemophilus influenzae beta-carbonic anhydrase complexed with bicarbonate
2A8D · Carbonic anhydrase 2: “Haemophilus influenzae beta-carbonic anhydrase complexed with bicarbonate”. X-ray diffraction, 3 ligands (BCT, ZN, SO4), 20 pockets (best druggability 0.77). MolNFT v1 #30744 on GenesisL1: 3D structure…
- PDB
- 2A8D
- Type
- protein
- Length
- 1,315 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carbonic anhydrase 2
- EC
- 4.2.1.1
- UniProt
- P45148
- Ligands
- BCT, ZN, SO4
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Carbonic anhydrase 2 (EC 4.2.1.1) | protein | 221 | 53% helix, 16% strand | P45148 |
| C, F | Carbonic anhydrase 2 (EC 4.2.1.1) | protein | 219 | 52% helix, 16% strand | P45148 |
| D | Carbonic anhydrase 2 (EC 4.2.1.1) | protein | 215 | 53% helix, 16% strand | P45148 |
| E | Carbonic anhydrase 2 (EC 4.2.1.1) | protein | 220 | 54% helix, 15% strand | P45148 |
Ligands and binding sites
- BCT · Bicarbonate ion · ligand · 6 copies · chains A, B, C, D, E, F
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 313 | 0.77 | 0.88 | 44 | SO4 |
| 2 | 325 | 0.77 | 0.88 | 45 | SO4 |
| 3 | 291 | 0.75 | 0.88 | 37 | empty |
| 4 | 198 | 0.55 | 0.79 | 30 | empty |
| 5 | 244 | 0.54 | 0.77 | 21 | empty |
Interfaces
8 interfaces between chains.
- D–F · 3305 Ų buried · 36 hydrogen bonds · protein-protein
- C–E · 3301 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 973 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 918 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 912 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 2A8D · Haemophilus influenzae beta-carbonic anhydrase complexed with bicarbonate · the same entry in another collection · chain F against F, TM-score 1.00
- P45148 · AlphaFold monomer V2.0 prediction for carbonic anhydrase 2 (P45148) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P45148
- Elsewhere: RCSB PDB 2A8D · PDBe 2A8D · UniProt P45148
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