Research workbench

Peridinin-chlorophyll-protein of amphidinium carterae

Analyse Peridinin-chlorophyll-protein of amphidinium carterae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1PPR
Type: protein
Length: 936 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peridinin-chlorophyll protein
UniProt: P80484
Ligands: PID, CLA, DGD
Pockets: 20 · best druggability 0.68

Structure

x-ray diffraction · 1 distinct chain · 73% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
M, N, O	Peridinin-chlorophyll protein	protein	312	73% helix, 1% strand	P80484

Ligands and binding sites

PID · Peridinin · ligand · 24 copies · chains M, N, O
CLA · Chlorophyll A · ligand · 6 copies · chains M, N, O
DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · 6 copies · chains M, N, O

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

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	589	0.68	0.77	65	PID
2	593	0.68	0.77	68	PID
3	465	0.66	0.78	40	PID
4	310	0.57	0.76	34	PID
5	228	0.56	0.78	35	PID

Interfaces

3 interfaces between chains.

N–O · 558 Å² buried · 2 hydrogen bonds · protein-protein
M–O · 558 Å² buried · 2 hydrogen bonds · protein-protein
M–N · 550 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

1PPR · Peridinin-chlorophyll-protein of amphidinium carterae · the same entry in another collection · chain M against M, TM-score 1.00
P80484 · AlphaFold monomer V2.0 prediction for peridinin-chlorophyll a-binding protein 1… · a predicted model of the same protein · chain M 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 P80484
Elsewhere: RCSB PDB 1PPR · PDBe 1PPR · UniProt P80484

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