MolNFT v1 · #189398 · protein
Phycocyanin rod structure of cyanobacterial phycobilisome
7VEB · C-phycocyanin alpha subunit: “Phycocyanin rod structure of cyanobacterial phycobilisome”. Electron microscopy, 1 ligand (CYC), 20 pockets (best druggability 0.88). MolNFT v1 #189398 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7VEB
- Type
- protein
- Length
- 4,537 residues
- Chains
- 27
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-phycocyanin alpha subunit; C-phycocyanin beta subunit; Phycobilisome 8.9 kda linker…
- UniProt
- P50032, P50033, P50035, P50034, P50040
- Ligands
- CYC
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 5 distinct chains · 54% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K, M, O, Q, S, U, W | C-phycocyanin alpha subunit | protein | 162 | 77% helix, 0% strand | P50032 |
| B, D, F, H, J, L, N, P, R, T, V, X | C-phycocyanin beta subunit | protein | 172 | 73% helix, 0% strand | P50033 |
| Y | Phycobilisome 8.9 kda linker polypeptide, phycocyanin- associated, rod | protein | 62 | 18% helix, 26% strand | P50035 |
| Z | Phycobilisome 32.1 kda linker polypeptide, phycocyanin- associated, rod | protein | 282 | 41% helix, 7% strand | P50034 |
| a | Phycobilisome rod-core linker polypeptide CPCG2 | protein | 185 | 49% helix, 1% strand | P50040 |
Ligands and binding sites
- CYC · Phycocyanobilin · ligand · 36 copies · chains A, D, B, Y, E, C, J, Z, G, L, F, H, I, K, M, P, N, Q, O, V, a, S, X, R, T, U, W
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 | 1081 | 0.88 | 0.90 | 111 | CYC |
| 2 | 1043 | 0.88 | 0.90 | 140 | empty |
| 3 | 578 | 0.87 | 0.92 | 71 | CYC |
| 4 | 654 | 0.86 | 0.90 | 81 | CYC |
| 5 | 533 | 0.84 | 0.90 | 46 | CYC |
Interfaces
97 interfaces between chains.
- O–P · 1653 Ų buried · 11 hydrogen bonds · protein-protein
- S–T · 1651 Ų buried · 7 hydrogen bonds · protein-protein
- K–L · 1648 Ų buried · 12 hydrogen bonds · protein-protein
- I–J · 1641 Ų buried · 7 hydrogen bonds · protein-protein
- G–H · 1640 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (nonstandard).
Compared structures
- 7VEB · Phycocyanin rod structure of cyanobacterial phycobilisome · the same entry in another collection · chain K against K, 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 P50032
- Every structure of UniProt P50033
- Every structure of UniProt P50035
- Every structure of UniProt P50034
- Every structure of UniProt P50040
- Elsewhere: RCSB PDB 7VEB · PDBe 7VEB · UniProt P50032 · UniProt P50033 · UniProt P50035 · UniProt P50034 · UniProt P50040
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