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Structure of the light harvesting complex PE545 from proteomonas sulcata

Analyse Structure of the light harvesting complex PE545 from proteomonas sulcata in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7TJA
Type: protein
Length: 2,056 residues
Chains: 18
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phycoerythrin alpha-subunit 1; Phycoerythrin alpha-subunit 2; Phycoerythrin beta-subunit
UniProt: A0A067YS87, A0A067YSJ2
Ligands: PEB, DBV, MG
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 14 distinct chains · 55% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Phycoerythrin alpha-subunit 1	protein	72	13% helix, 64% strand	A0A067YS87
Q	Phycoerythrin alpha-subunit 2	protein	61	20% helix, 69% strand	A0A067YSJ2
B	Phycoerythrin beta-subunit	protein	167	71% helix, 2% strand	—
C	Phycoerythrin alpha-subunit 2	protein	60	20% helix, 70% strand	A0A067YSJ2
R	Phycoerythrin alpha-subunit 1	protein	70	0% helix, 70% strand	A0A067YS87
D	Phycoerythrin beta-subunit	protein	174	68% helix, 2% strand	—
E, M	Phycoerythrin alpha-subunit 1	protein	74	20% helix, 24% strand	A0A067YS87
G, K, O	Phycoerythrin alpha-subunit 2	protein	67	27% helix, 27% strand	A0A067YSJ2
F	Phycoerythrin beta-subunit	protein	166	71% helix, 2% strand	—
H	Phycoerythrin beta-subunit	protein	173	72% helix, 2% strand	—
I	Phycoerythrin alpha-subunit 1	protein	75	20% helix, 24% strand	A0A067YS87
J, L	Phycoerythrin beta-subunit	protein	173	72% helix, 2% strand	—
N	Phycoerythrin beta-subunit	protein	170	71% helix, 2% strand	—
P	Phycoerythrin beta-subunit	protein	173	72% helix, 2% strand	—

Ligands and binding sites

PEB · Phycoerythrobilin · ligand · 24 copies · chains A, Q, B, R, D, C, E, F, H, G, I, J, L, K, M, N, P, O
DBV · 15,16-dihydrobiliverdin · ligand · 10 copies · chains A, Q, B, C, R, D, E, G, F, H, I, K, J, L, M, O, N, P
MG · Magnesium ion · metal · chains K, J

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	666	0.87	0.91	105	PEB
2	1113	0.84	0.85	127	DBV, PEB
3	722	0.84	0.88	85	PEB, MG
4	852	0.84	0.86	96	PEB
5	1154	0.75	0.78	118	DBV

Interfaces

51 interfaces between chains.

C–R · 2759 Å² buried · 515 hydrogen bonds · protein-protein
A–Q · 2732 Å² buried · 531 hydrogen bonds · protein-protein
I–J · 2254 Å² buried · 23 hydrogen bonds · protein-protein
M–N · 2250 Å² buried · 24 hydrogen bonds · protein-protein
E–F · 2242 Å² buried · 21 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 32 cofactor, 14 covalent, 2 disulfide, 2 isopeptide (phycoerythrobilin attachment, covalent ligand, disulfide, isopeptide).

Compared structures

7TJA · Structure of the Light Harvesting Complex PE545 from Proteomonas sulcata · 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 A0A067YS87
Every structure of UniProt A0A067YSJ2
Elsewhere: RCSB PDB 7TJA · PDBe 7TJA · UniProt A0A067YS87 · UniProt A0A067YSJ2

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