MolNFT v1 · #103690 · protein
Crystal structure of allophycocyanin B from synechocystis pcc 6803
4PO5 · Allophycocyanin subunit alpha-B: “Crystal structure of allophycocyanin B from synechocystis pcc 6803”. X-ray diffraction, 2 ligands (CYC, SO4), 10 pockets (best druggability 0.79). MolNFT v1 #103690 on GenesisL1: 3D structure…
- PDB
- 4PO5
- Type
- protein
- Length
- 969 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Allophycocyanin subunit alpha-B; Allophycocyanin beta chain
- UniProt
- P72870, Q01952
- Ligands
- CYC, SO4
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Allophycocyanin subunit alpha-B | protein | 162 | 79% helix, 0% strand | P72870 |
| B, D, F | Allophycocyanin beta chain | protein | 161 | 78% helix, 0% strand | Q01952 |
Ligands and binding sites
- CYC · Phycocyanobilin · ligand · 6 copies · chains A, F, B, C, D, E
- SO4 · Sulfate ion · ion · 21 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 315 | 0.79 | 0.89 | 46 | CYC |
| 2 | 321 | 0.78 | 0.88 | 42 | CYC |
| 3 | 302 | 0.77 | 0.89 | 43 | CYC |
| 4 | 156 | 0.57 | 0.82 | 28 | CYC |
| 5 | 134 | 0.57 | 0.82 | 25 | CYC |
Interfaces
9 interfaces between chains.
- A–B · 1525 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1525 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1514 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 667 Ų buried · 10 hydrogen bonds · protein-protein
- A–F · 666 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 cofactor, 3 modified (phycocyanobilin attachment, nonstandard).
Compared structures
- 4PO5 · Crystal structure of allophycocyanin B from Synechocystis PCC 6803 · the same entry in another collection · chain F against F, TM-score 1.00
- Q01952 · AlphaFold monomer V2.0 prediction for allophycocyanin beta chain (Q01952) · a predicted model of the same protein · chain D against A, TM-score 0.99
- P72870 · AlphaFold monomer V2.0 prediction for allophycocyanin subunit alpha-B (P72870) · a predicted model of the same protein · chain E against A, TM-score 0.96
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 P72870
- Every structure of UniProt Q01952
- Elsewhere: RCSB PDB 4PO5 · PDBe 4PO5 · UniProt P72870 · UniProt Q01952
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