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Atomic resolution structure of C-phycoerythrin from marine cyanobacterium phormidium sp. A09DM at pH 7.5
Analyse Atomic resolution structure of C-phycoerythrin from marine cyanobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NB4
- Type
- protein
- Length
- 4,176 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phycoerythrin alpha SUBUNIT,PHYCOERYTHRIN alpha subunit, phycoerythrin alpha…
- UniProt
- A0A0E3W010, A0A0E4G455
- Ligands
- PEB, NA, PI, NO3
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Phycoerythrin alpha SUBUNIT,PHYCOERYTHRIN alpha subunit, phycoerythrin alpha SUBUNIT,PHYCOERYTHRIN alpha SUBUNIT,PHYCOERYTHRIN alpha subunit | protein | 164 | 77% helix, 0% strand | A0A0E3W010 |
| M, N, O, P, Q, R, S, T, U, V, W, X | Phycoerythrin beta SUBUNIT,PHYCOERYTHRIN beta subunit | protein | 184 | 73% helix, 0% strand | A0A0E4G455 |
Ligands and binding sites
- PEB · Phycoerythrobilin · ligand · 60 copies · chains A, O, B, M, C, N, D, Q, E, R, F, P, G, U, H, S, I, T, J, W, K, X, L, V
- NA · Sodium ion · metal · 16 copies · chains A, P, B, Q, C, R, D, M, E, N, F, O, G, V, H, W, I, X, J, S, K, T, L, U
- PI · Hydrogenphosphate ion · ion · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
- NO3 · Nitrate ion · ion · 6 copies · chains A, F, C, E, B, D, I, K, H, J, G, L
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 10 copies · chains B, N, A, M, C, O, D, P, E, Q, F, R, G, S, I, U, K, W, L, X
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 2 copies · chains H, T, J, V
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 | 968 | 0.89 | 0.90 | 129 | PEB, NO3 |
| 2 | 1162 | 0.88 | 0.89 | 139 | PEB, NO3 |
| 3 | 1140 | 0.87 | 0.88 | 139 | PEB, NO3 |
| 4 | 1099 | 0.87 | 0.88 | 133 | PEB, NO3 |
| 5 | 1149 | 0.87 | 0.88 | 144 | PEB, NO3 |
Interfaces
61 interfaces between chains.
- E–Q · 1506 Ų buried · 14 hydrogen bonds · protein-protein
- G–S · 1505 Ų buried · 14 hydrogen bonds · protein-protein
- J–V · 1503 Ų buried · 16 hydrogen bonds · protein-protein
- A–M · 1498 Ų buried · 14 hydrogen bonds · protein-protein
- D–P · 1494 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 72 cofactor, 12 modified, 7 covalent (phycoerythrobilin attachment, nonstandard, additive adduct).
Compared structures
- 5NB4 · Atomic resolution structure of C-phycoerythrin from marine cyanobacterium Phormidium sp.… · the same entry in another collection · chain A against A, 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 A0A0E3W010
- Every structure of UniProt A0A0E4G455
- Elsewhere: RCSB PDB 5NB4 · PDBe 5NB4 · UniProt A0A0E3W010 · UniProt A0A0E4G455
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