Research workbench
Top cylinder bound to OCP from high-resolution phycobilisome quenched by OCP (local refinement)
Analyse Top cylinder bound to OCP from high-resolution phycobilisome quenched by OCP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8TPJ
- Type
- protein
- Length
- 2,726 residues
- Chains
- 20
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.1
- Source
- Synechocystis sp. PCC 6803
- Molecule
- Phycobiliprotein ApcE; Orange carotenoid-binding protein; Phycobilisome 7.8 kDa linker…
- UniProt
- Q55544, P74102, Q02925, Q01951, Q01952, P73093
- Ligands
- CYC, 45D
- Pockets
- 20 · best druggability 0.90
Structure
electron microscopy · resolution 2.1 · 10 distinct chains · 51% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phycobiliprotein ApcE | protein | 210 | 52% helix, 1% strand | Q55544 |
| B | Orange carotenoid-binding protein | protein | 296 | 45% helix, 17% strand | P74102 |
| b | Orange carotenoid-binding protein | protein | 130 | 24% helix, 36% strand | P74102 |
| C | Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core | protein | 67 | 24% helix, 34% strand | Q02925 |
| D, F, H, J, L, N | Allophycocyanin alpha chain | protein | 160 | 80% helix, 0% strand | Q01951 |
| E, G, I, K, M, O | Allophycocyanin beta chain | protein | 161 | 77% helix, 0% strand | Q01952 |
| P | Phycobilisome rod-core linker polypeptide CpcG | protein | 41 | 44% helix, 0% strand | P73093 |
| Q | Phycobilisome rod-core linker polypeptide CpcG | protein | 42 | 43% helix, 0% strand | P73093 |
| R | Phycobilisome rod-core linker polypeptide CpcG | protein | 4 | 0% helix, 0% strand | P73093 |
| S | Phycobilisome rod-core linker polypeptide CpcG | protein | 10 | 0% helix, 0% strand | P73093 |
Ligands and binding sites
- CYC · Phycocyanobilin · ligand · 12 copies · chains D, I, A, E, F, P, C, G, H, J, K, S, L, M, N, O, R
- 45D · beta,beta-carotene-4,4'-dione · ligand · chains B, D
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 | 931 | 0.90 | 0.93 | 127 | 45D, CYC |
| 2 | 403 | 0.85 | 0.93 | 58 | CYC |
| 3 | 530 | 0.84 | 0.90 | 59 | CYC |
| 4 | 742 | 0.84 | 0.87 | 79 | CYC |
| 5 | 568 | 0.84 | 0.90 | 74 | empty |
Interfaces
69 interfaces between chains.
- D–E · 1511 Ų buried · 18 hydrogen bonds · protein-protein
- K–L · 1505 Ų buried · 15 hydrogen bonds · protein-protein
- H–I · 1494 Ų buried · 17 hydrogen bonds · protein-protein
- M–N · 1488 Ų buried · 17 hydrogen bonds · protein-protein
- J–O · 1464 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 cofactor, 6 modified (phycocyanobilin attachment, nonstandard).
Compared structures
- Q01952 · AlphaFold monomer V2.0 prediction for allophycocyanin beta chain (Q01952) · a predicted model of the same protein · chain I 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 D against A, TM-score 0.97
- Q02925 · AlphaFold monomer V2.0 prediction for phycobilisome 7.8 kda linker polypeptide… · a predicted model of the same protein · chain C against A, TM-score 0.97
- Q55544 · AlphaFold monomer V2.0 prediction for phycobiliprotein apce (Q55544) · a predicted model of the same protein · chain A against A, TM-score 0.94
- P74102 · AlphaFold monomer V2.0 prediction for orange carotenoid-binding protein (P74102) · a predicted model of the same protein · chain b against A, TM-score 0.88
- P73093 · AlphaFold monomer V2.0 prediction for phycobilisome rod-core linker polypeptide cpcg… · a predicted model of the same protein · chain R against A, TM-score 0.84
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 Q55544
- Every structure of UniProt P74102
- Every structure of UniProt Q02925
- Every structure of UniProt Q01951
- Every structure of UniProt Q01952
- Every structure of UniProt P73093
- Elsewhere: RCSB PDB 8TPJ · PDBe 8TPJ · UniProt Q55544 · UniProt P74102 · UniProt Q02925 · UniProt Q01951 · UniProt Q01952 · UniProt P73093
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