Research workbench
X-ray crystal structure of phycocyanin from synechococcus elongatus sp. pcc 7942
Analyse X-ray crystal structure of phycocyanin from synechococcus elongatus sp. pcc 7942 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4H0M
- Type
- protein
- Length
- 4,008 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-phycocyanin alpha chain; C-phycocyanin beta chain
- UniProt
- P13530, P06539
- Ligands
- CYC
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K, M, O, Q, S, U, W | C-phycocyanin alpha chain | protein | 162 | 78% helix, 0% strand | P13530 |
| B, D, F, H, J, L, N, P, R, T, V, X | C-phycocyanin beta chain | protein | 172 | 76% helix, 0% strand | P06539 |
Ligands and binding sites
- CYC · Phycocyanobilin · ligand · 36 copies · chains A, D, B, K, C, F, I, E, G, J, H, L, M, P, N, W, O, R, U, Q, S, V, T, X
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 | 1073 | 0.83 | 0.84 | 112 | CYC |
| 2 | 356 | 0.80 | 0.89 | 39 | CYC |
| 3 | 336 | 0.80 | 0.90 | 38 | CYC |
| 4 | 355 | 0.80 | 0.89 | 37 | CYC |
| 5 | 440 | 0.80 | 0.87 | 42 | CYC |
Interfaces
63 interfaces between chains.
- O–P · 1678 Ų buried · 15 hydrogen bonds · protein-protein
- K–L · 1650 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1642 Ų buried · 10 hydrogen bonds · protein-protein
- U–V · 1634 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1626 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 34 cofactor, 12 modified (phycocyanobilin attachment, nonstandard).
Compared structures
- 4H0M · X-Ray Crystal Structure of Phycocyanin from Synechococcus elongatus sp. PCC 7942 · the same entry in another collection · chain E against E, 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 P13530
- Every structure of UniProt P06539
- Elsewhere: RCSB PDB 4H0M · PDBe 4H0M · UniProt P13530 · UniProt P06539
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