Structure of PDB 5mdx Chain 1

Receptor sequence

>5mdx1 (length=219) Species: 3702 (Arabidopsis thaliana) [Search protein sequence]

SPWYGSDRVKYLGPFSGESPSYLTGEFPGDYGWDTAGLSADPETFARNRE
LEVIHSRWAMLGALGCVFPELLARNGVKFGEAVWFKAGSQIFSDGGLDYL
GNPSLVHAQSILAIWATQVILMGAVEGYRVAGNGPLGEAEDLLYPGGSFD
PLGLATDPEAFAELKVKELKNGRLAMFSMFGFFVQAIVTGKGPIENLADH
LADPVNNNAWAFATNFVPG

3D structure

PDB

5mdx Subunit and chlorophyll organization of the plant photosystem II supercomplex.

Chain

Resolution

5.3 Å

3D
structure

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Enzymatic activity

Enzyme Commision number

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	CHL	1	K57 Y58 P61 W80	K10 Y11 P14 W33
BS02	CLA	1	G76 D77 Y78 W80 D81 F92 N95 E99 H102 R220 M223	G29 D30 Y31 W33 D34 F45 N48 E52 H55 R173 M176
BS03	CLA	1	L108 G112 F115 Y146 L147	L61 G65 F68 Y99 L100
BS04	CHL	1	S151 L152 V153 H154 Q156 S157 I161	S104 L105 V106 H107 Q109 S110 I114
BS05	CHL	1	I161 Q165	I114 Q118
BS06	CHL	1	F132 K133	F85 K86
BS07	CHL	1	R104 W105 Y175 R176 G181 L183 G184 P192 F196	R57 W58 Y128 R129 G134 L136 G137 P145 F149
BS08	CHL	1	I101 W105 M169 G170 E173	I54 W58 M122 G123 E126
BS09	CLA	1	R104 M107 Y191 P192 G193 F196 D197 F208 E215 N218	R57 M60 Y144 P145 G146 F149 D150 F161 E168 N171
BS10	CLA	1	W50 K214 K217	W3 K167 K170
BS11	CLA	1	K214 N218 L221	K167 N171 L174
BS12	CLA	1	F224 G228 Q232 T236 N243 H247 N255 A256	F177 G181 Q185 T189 N196 H200 N208 A209
BS13	CLA	1	H247 P251 N255	H200 P204 N208
BS14	CHL	1	A260 N262 F263 V264 P265	A213 N215 F216 V217 P218
BS15	CHL	1	W80 T82	W33 T35

Gene Ontology

	Biological Process
GO:0009765	photosynthesis, light harvesting

	Cellular Component
GO:0016020	membrane

View graph for
Biological Process

View graph for
Cellular Component

External links

PDB	RCSB:5mdx, PDBe:5mdx, PDBj:5mdx
PDBsum	5mdx
PubMed	28604725
UniProt	P04778\|CB1C_ARATH Chlorophyll a-b binding protein 1, chloroplastic (Gene Name=LHCB1.3)

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