Research workbench
B-cylinder of Synechocystis PCC 6803 Phycobilisome, complex with OCP - local refinement
Analyse B-cylinder of Synechocystis PCC 6803 Phycobilisome, complex with OCP - local… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SCB
- Type
- protein
- Length
- 4,743 residues
- Chains
- 29
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.5
- Source
- Synechocystis sp. PCC 6803 substr. Kazusa
- Molecule
- Allophycocyanin alpha chain; Allophycocyanin beta chain; Allophycocyanin subunit alpha-B…
- EC
- 4.-.-.-
- UniProt
- Q01951, Q01952, P72870, P74551, Q01950, Q55544, P73093, P74102, P74135
- Ligands
- CYC, 45D
- Pockets
- 20 · best druggability 0.91
Structure
electron microscopy · resolution 2.5 · 9 distinct chains · 59% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| AA, AC, AH, AJ, AN, AP, AR, AU, AW, AY | Allophycocyanin alpha chain | protein | 160 | 78% helix, 0% strand | Q01951 |
| AB, AD, AF, AI, AL, AO, AQ, AS, AV, AX, AZ | Allophycocyanin beta chain | protein | 161 | 76% helix, 0% strand | Q01952 |
| AE | Allophycocyanin subunit alpha-B | protein | 160 | 76% helix, 0% strand | P72870 |
| AK | Allophycocyanin subunit beta-18 | protein | 169 | 75% helix, 0% strand | P74551 |
| BB, BC | Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core | protein | 67 | 25% helix, 31% strand | Q01950 |
| BE | Phycobiliprotein ApcE (EC 4.-.-.-) | protein | 647 | 50% helix, 3% strand | Q55544 |
| BG | Phycobilisome rod-core linker polypeptide CpcG | protein | 57 | 25% helix, 0% strand | P73093 |
| BH | Orange carotenoid-binding protein | protein | 169 | 55% helix, 1% strand | P74102 |
| BI | Sll1873 protein | protein | 36 | 33% helix, 0% strand | P74135 |
Ligands and binding sites
- CYC · Phycocyanobilin · ligand · 24 copies · chains AA, AF, AB, BE, AC, AD, BB, AE, AH, AL, AI, AJ, AK, AN, AS, BI, AO, AP, AQ, AR, BH, AU, AZ, AV, BC, AW, AX, AY
- 45D · beta,beta-carotene-4,4'-dione · ligand · chains AR, BH
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 906 | 0.91 | 0.94 | 125 | CYC, 45D |
| 2 | 983 | 0.89 | 0.91 | 120 | CYC |
| 3 | 1015 | 0.89 | 0.90 | 129 | CYC |
| 4 | 840 | 0.89 | 0.92 | 91 | CYC |
| 5 | 831 | 0.88 | 0.91 | 84 | CYC |
Interfaces
112 interfaces between chains.
- AL–BE · 2458 Ų buried · 25 hydrogen bonds · protein-protein
- AK–BE · 1797 Ų buried · 23 hydrogen bonds · protein-protein
- AI–BE · 1615 Ų buried · 27 hydrogen bonds · protein-protein
- AU–AV · 1594 Ų buried · 11 hydrogen bonds · protein-protein
- AA–AB · 1587 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 cofactor (phycocyanobilin attachment).
Compared structures
- Q01952 · AlphaFold monomer V2.0 prediction for allophycocyanin beta chain (Q01952) · a predicted model of the same protein · chain AI against A, TM-score 0.99
- Q01951 · AlphaFold monomer V2.0 prediction for allophycocyanin alpha chain (Q01951) · a predicted model of the same protein · chain AA against A, TM-score 0.98
- P74551 · AlphaFold monomer V2.0 prediction for allophycocyanin subunit beta-18 (P74551) · a predicted model of the same protein · chain AK against A, TM-score 0.97
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 Q01951
- Every structure of UniProt Q01952
- Every structure of UniProt P72870
- Every structure of UniProt P74551
- Every structure of UniProt Q01950
- Every structure of UniProt Q55544
- Every structure of UniProt P73093
- Every structure of UniProt P74102
- Every structure of UniProt P74135
- Elsewhere: RCSB PDB 7SCB · PDBe 7SCB · UniProt Q01951 · UniProt Q01952 · UniProt P72870 · UniProt P74551 · UniProt Q01950 · UniProt Q55544 · UniProt P73093 · UniProt P74102 · UniProt P74135
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