MolNFT v1 · #141523 · protein
Crystal structure of CF3-aequorin
5ZAB · Aequorin-2: “Crystal structure of CF3-aequorin”. X-ray diffraction, 1 ligand (9A3), 20 pockets (best druggability 0.85). MolNFT v1 #141523 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5ZAB
- Type
- protein
- Length
- 3,051 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aequorin-2
- UniProt
- P02592
- Ligands
- 9A3
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 61% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, H, I, J, K, M, N, O | Aequorin-2 | protein | 191 | 61% helix, 5% strand | P02592 |
| B, F | Aequorin-2 | protein | 192 | 60% helix, 5% strand | P02592 |
| G | Aequorin-2 | protein | 190 | 62% helix, 6% strand | P02592 |
| L, P | Aequorin-2 | protein | 188 | 62% helix, 5% strand | P02592 |
Ligands and binding sites
- 9A3 · (2S)-8-benzyl-2-hydroperoxy-6-(4-hydroxyphenyl)-2-{[4-(trifluoromethyl)phenyl]methyl}imidazo[1,2-a]pyrazin-3(2H)-one · ligand · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 209 | 0.85 | 0.97 | 32 | 9A3 |
| 2 | 211 | 0.85 | 0.97 | 32 | 9A3 |
| 3 | 221 | 0.85 | 0.97 | 33 | 9A3 |
| 4 | 210 | 0.85 | 0.97 | 32 | 9A3 |
| 5 | 204 | 0.85 | 0.97 | 33 | 9A3 |
Interfaces
22 interfaces between chains.
- F–G · 1057 Ų buried · 23 hydrogen bonds · protein-protein
- I–J · 1057 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 1051 Ų buried · 25 hydrogen bonds · protein-protein
- M–N · 1039 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1020 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 5ZAB · Crystal structure of cf3-aequorin · the same entry in another collection · chain I against I, 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 P02592
- Elsewhere: RCSB PDB 5ZAB · PDBe 5ZAB · UniProt P02592
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