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Structure of the photoacclimated light harvesting complex PE545 from proteomonas sulcata

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

PDB: 7TLF
Type: protein
Length: 1,912 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phycoerythrin alpha-subunit 1; Phycoerythrin beta-subunit; Phycoerythrin alpha-subunit 2
UniProt: A0A067YS87, A0A067YSJ2
Ligands: PEB, DBV
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 13 distinct chains · 62% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Phycoerythrin alpha-subunit 1	protein	72	21% helix, 25% strand	A0A067YS87
B	Phycoerythrin beta-subunit	protein	162	72% helix, 2% strand	—
C	Phycoerythrin alpha-subunit 2	protein	60	27% helix, 30% strand	A0A067YSJ2
D	Phycoerythrin beta-subunit	protein	173	71% 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	170	72% helix, 2% strand	—
I	Phycoerythrin alpha-subunit 1	protein	75	20% helix, 24% strand	A0A067YS87
J	Phycoerythrin beta-subunit	protein	170	72% helix, 2% strand	—
L	Phycoerythrin beta-subunit	protein	172	73% 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, B, C, D, E, F, G, H, I, J, L, K, P, M, N, O
DBV · 15,16-dihydrobiliverdin · ligand · 8 copies · chains A, B, C, D, E, G, F, H, I, K, J, L, M, O, N, P

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	766	0.85	0.88	91	PEB
2	1103	0.84	0.85	123	DBV, PEB
3	830	0.84	0.87	92	PEB
4	752	0.82	0.86	96	PEB
5	1169	0.74	0.77	111	DBV

Interfaces

35 interfaces between chains.

I–J · 2235 Å² buried · 22 hydrogen bonds · protein-protein
M–N · 2215 Å² buried · 20 hydrogen bonds · protein-protein
E–F · 2196 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 2075 Å² buried · 15 hydrogen bonds · protein-protein
K–L · 1970 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 32 cofactor, 8 covalent (phycoerythrobilin attachment, covalent ligand).

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 7TLF · PDBe 7TLF · UniProt A0A067YS87 · UniProt A0A067YSJ2

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