MolNFT v1 · #127926 · protein
High resolution C-phycoerythrin from marine cyanobacterium phormidium sp. A09DM at pH 7.5
5NB3 · Phycoerythrin alpha SUBUNIT,PHYCOERYTHRIN alpha subunit…: “High resolution C-phycoerythrin from marine cyanobacterium phormidium sp. A09DM at pH 7.5”. X-ray diffraction, 3 ligands (PEB, NA, CL), 20 pockets (best druggability 0.87).…
- PDB
- 5NB3
- 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 subunit…
- UniProt
- A0A0E3W010, A0A0E4G455
- Ligands
- PEB, NA, CL
- Pockets
- 20 · best druggability 0.87
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 | protein | 164 | 78% helix, 0% strand | A0A0E3W010 |
| M, N, O, P, Q, R, S, T, U, V, W, X | Phycoerythrin beta SUBUNIT,PHYCOERYTHRIN beta subunit | protein | 184 | 72% 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 · 19 copies · chains A, F, P, B, Q, C, R, D, M, E, N, O, G, L, V, H, W, I, X, J, S, K, T, U
- CL · Chloride ion · ion · 6 copies · chains A, F, B, D, C, E, I, K, H, J, G, L
- FMT · Formic acid · additive · 15 copies · chains A, C, H, J, K, N, O, P, Q, U, V, W
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 12 copies · chains A, M, B, N, 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 | 869 | 0.87 | 0.90 | 110 | CL, PEB |
| 2 | 803 | 0.86 | 0.89 | 108 | PEB, CL |
| 3 | 866 | 0.86 | 0.88 | 102 | CL, PEB |
| 4 | 731 | 0.86 | 0.90 | 91 | CL, PEB |
| 5 | 520 | 0.82 | 0.89 | 75 | CL |
Interfaces
61 interfaces between chains.
- J–V · 1519 Ų buried · 15 hydrogen bonds · protein-protein
- E–Q · 1518 Ų buried · 14 hydrogen bonds · protein-protein
- H–T · 1516 Ų buried · 16 hydrogen bonds · protein-protein
- G–S · 1515 Ų buried · 14 hydrogen bonds · protein-protein
- K–W · 1510 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 69 cofactor, 12 modified, 4 covalent (phycoerythrobilin attachment, nonstandard, additive adduct).
Compared structures
- 5NB3 · High resolution C-phycoerythrin from marine cyanobacterium Phormidium sp. A09DM at pH 7.5 · the same entry in another collection · chain C against C, 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 5NB3 · PDBe 5NB3 · UniProt A0A0E3W010 · UniProt A0A0E4G455
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