Research workbench
Crystal structure of the apoaequorin complex with (S)-dactz
Analyse Crystal structure of the apoaequorin complex with (S)-dactz in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EG2
- 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
- J2X
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 61% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, J, P | Aequorin-2 | protein | 192 | 60% helix, 6% strand | P02592 |
| D, H, I, M, N | Aequorin-2 | protein | 190 | 61% helix, 6% strand | P02592 |
| F, G, O | Aequorin-2 | protein | 191 | 61% helix, 5% strand | P02592 |
| K, L | Aequorin-2 | protein | 188 | 62% helix, 6% strand | P02592 |
Ligands and binding sites
- J2X · (2~{S})-2-(hydroxymethyl)-6-(4-hydroxyphenyl)-2-[(4-hydroxyphenyl)methyl]-4-(phenylmethyl)-3~{H}-inden-1-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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 223 | 0.85 | 0.97 | 33 | J2X |
| 2 | 210 | 0.85 | 0.97 | 30 | J2X |
| 3 | 207 | 0.85 | 0.97 | 30 | J2X |
| 4 | 212 | 0.85 | 0.97 | 30 | J2X |
| 5 | 210 | 0.85 | 0.97 | 31 | J2X |
Interfaces
20 interfaces between chains.
- C–O · 1081 Ų buried · 19 hydrogen bonds · protein-protein
- B–H · 1062 Ų buried · 16 hydrogen bonds · protein-protein
- A–G · 1056 Ų buried · 16 hydrogen bonds · protein-protein
- B–I · 1036 Ų buried · 17 hydrogen bonds · protein-protein
- D–P · 1026 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 7EG2 · Crystal structure of the apoAequorin complex with (S)-daCTZ · the same entry in another collection · chain J against J, 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 7EG2 · PDBe 7EG2 · UniProt P02592
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