MolNFT v1 · #61100 · protein
Allophycocyanin from thermosynechococcus vulcanus
3DBJ: “Allophycocyanin from thermosynechococcus vulcanus”. X-ray diffraction, 1 ligand (CYC), 13 pockets (best druggability 0.81). MolNFT v1 #61100 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3DBJ
- Type
- protein
- Length
- 1,284 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Allophycocyanin
- UniProt
- B3VNK2, B3VNK3
- Ligands
- CYC
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Allophycocyanin | protein | 160 | 76% helix, 0% strand | B3VNK2 |
| B, D, F, H | Allophycocyanin | protein | 161 | 74% helix, 0% strand | B3VNK3 |
Ligands and binding sites
- CYC · Phycocyanobilin · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 941 | 0.81 | 0.83 | 100 | empty |
| 2 | 102 | 0.61 | 0.87 | 19 | CYC |
| 3 | 100 | 0.60 | 0.87 | 21 | CYC |
| 4 | 98 | 0.59 | 0.86 | 18 | CYC |
| 5 | 158 | 0.58 | 0.82 | 30 | CYC |
Interfaces
6 interfaces between chains.
- A–B · 1548 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1547 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1546 Ų buried · 13 hydrogen bonds · protein-protein
- G–H · 1546 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 836 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor, 4 modified (phycocyanobilin attachment, nonstandard).
Compared structures
- 3DBJ · Allophycocyanin from Thermosynechococcus vulcanus · 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
- Every structure of UniProt B3VNK2
- Every structure of UniProt B3VNK3
- Elsewhere: RCSB PDB 3DBJ · PDBe 3DBJ · UniProt B3VNK2 · UniProt B3VNK3
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