Research workbench
Crystal structure of the reassembled venus
Analyse Crystal structure of the reassembled venus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AKO
- Type
- protein
- Length
- 898 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Venus
- Ligands
- CR2, SO4
- Pockets
- 15 · best druggability 0.53
Structure
x-ray diffraction · 6 distinct chains · 7% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Venus | protein | 152 | 14% helix, 47% strand | — |
| B | Venus | protein | 80 | 0% helix, 55% strand | — |
| C, E, G | Venus | protein | 149 | 14% helix, 47% strand | — |
| D | Venus | protein | 76 | 0% helix, 58% strand | — |
| F | Venus | protein | 72 | 0% helix, 61% strand | — |
| H | Venus | protein | 71 | 0% helix, 62% strand | — |
Ligands and binding sites
- CR2 · {(4Z)-2-(aminomethyl)-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 4 copies · chains A, B, C, D, E, F, G, H
- SO4 · Sulfate ion · ion · chains C
- PE8 · 3,6,9,12,15,18,21-heptaoxatricosane-1,23-diol · additive · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 235 | 0.53 | 0.77 | 38 | empty |
| 2 | 233 | 0.51 | 0.76 | 31 | empty |
| 3 | 203 | 0.50 | 0.76 | 29 | empty |
| 4 | 209 | 0.49 | 0.76 | 33 | empty |
| 5 | 168 | 0.45 | 0.75 | 21 | empty |
Interfaces
13 interfaces between chains.
- E–F · 3284 Ų buried · 68 hydrogen bonds · protein-protein
- C–D · 3283 Ų buried · 67 hydrogen bonds · protein-protein
- A–B · 3243 Ų buried · 63 hydrogen bonds · protein-protein
- G–H · 3236 Ų buried · 62 hydrogen bonds · protein-protein
- D–H · 468 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor (chromophore).
Compared structures
- 3AKO · Crystal Structure of the Reassembled Venus · the same entry in another collection · chain A against A, 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
- Elsewhere: RCSB PDB 3AKO · PDBe 3AKO
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