MolNFT v1 · #81864 · protein

Crystal structure of the B-phycoerythrin from the red algae porphyridium cruentum at PH5

3V58 · Phycoerythrin alpha subunit: “Crystal structure of the B-phycoerythrin from the red algae porphyridium cruentum at PH5”. X-ray diffraction, 2 ligands (PEB, SO4), 14 pockets (best druggability 0.64). MolNFT v1 #81864 on GenesisL1: 3D…

PDB: 3V58
Type: protein
Length: 682 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phycoerythrin alpha subunit; Phycoerythrin beta subunit
UniProt: E2IH77, E2IH76
Ligands: PEB, SO4
Pockets: 14 · best druggability 0.64

Structure

x-ray diffraction · 2 distinct chains · 76% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Phycoerythrin alpha subunit	protein	164	77% helix, 0% strand	E2IH77
B, D	Phycoerythrin beta subunit	protein	177	74% helix, 0% strand	E2IH76

Ligands and binding sites

PEB · Phycoerythrobilin · ligand · 10 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	98	0.64	0.89	23	PEB
2	131	0.62	0.86	32	PEB
3	226	0.60	0.80	33	empty
4	81	0.59	0.88	14	empty
5	203	0.58	0.80	28	empty

Interfaces

5 interfaces between chains.

C–D · 1603 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1602 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 1055 Å² buried · 18 hydrogen bonds · protein-protein
B–C · 327 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 325 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 cofactor, 2 modified (phycoerythrobilin attachment, nonstandard).

Compared structures

3V58 · Crystal Structure of the B-phycoerythrin from the red algae Porphyridium Cruentum at pH5 · 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 E2IH77
Every structure of UniProt E2IH76
Elsewhere: RCSB PDB 3V58 · PDBe 3V58 · UniProt E2IH77 · UniProt E2IH76

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