5DPR - JenaLib

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Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF PLEKHM1 LIR-FUSED HUMAN LC3A_2-121

Authors :   A. C. Ravichandran, H. Suzuki, R. C. J. Dobson

Date :   14 Sep 15 (Deposition) - 28 Sep 16 (Release) - 28 Sep 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Autophagy; Plekhm1; Atg8; Lc3; Gabarap, Chimeric Protein, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. C. Ravichandran, H. Suzuki, R. C. J. Dobson
Crystal Structure Of Plekhm1 Lir-Fused Human Lc3A_2-121
To Be Published
PubMed: search

Molecule 1 - PLECKSTRIN HOMOLOGY DOMAIN-CONTAINING FAMILY M MEMBER 1, MICROTUBULE-ASSOCIATED PROTEINS 1A/1B LIGHT CHAIN 3A
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET30
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP Q9Y4G2 RESIDUES 627-638, UNP Q9H492 RESIDUES 2-121,UNP Q9Y4G2 RESIDUES 627-638, UNP Q9H492 RESIDUES 2-121
	Gene	:	PLEKHM1, KIAA0356, MAP1LC3A
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PH DOMAIN-CONTAINING FAMILY M MEMBER 1,162 KDA ADAPTER PROTEIN,AP162,AUTOPHAGY-RELATED PROTEIN LC3 A,AUTOPHAGY-RELATED UBIQUITIN-LIKE MODIFIER LC3 A,MAP1 LIGHT CHAIN 3-LIKE PROTEIN 1, MAP1A/MAP1B LIGHT CHAIN 3 A,MAP1A/MAP1B LC3 A,MICROTUBULE-ASSOCIATED PROTEIN 1 LIGHT CHAIN 3 ALPHA

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 5DPR)

(no "Site" information available for 5DPR)

(no "SS Bond" information available for 5DPR)

Asymmetric Unit

No.	Residues
1	Gly A:11	-	Ser A:12
2	Ser B:14	-	Asp B:15
3	Gly C:11	-	Ser C:12
4	Pro C:13	-	Ser C:14
5	Ser C:101	-	Val C:102
6	Ser D:12	-	Pro D:13

(no "SAP(SNP)/Variant" information available for 5DPR)

(no "PROSITE Motif" information available for 5DPR)

(no "Exon" information available for 5DPR)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:124
                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.............eeeee...hhhhhhhhhhhhh........eee...........hhhhhhhhhh.....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dpr A   6 EWVNVGSPSDRPFKQRRSFADRCKEVQQIRDQHPSKIPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELVKIIRRRLQLNPTQAFFLLVNQHSMVSVSTPIADIYEQEKDEDGFLYMVYASQET 129
                                    15        25        35        45        55        65        75        85        95       105       115       125

Chain B from PDB  Type:PROTEIN  Length:127
                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.............eeeee...hhhhhhhhhhhhh........eeee..........hhhhhhhhhh.....eeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dpr B   6 EWVNVGSPSDRPFKQRRSFADRCKEVQQIRDQHPSKIPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELVKIIRRRLQLNPTQAFFLLVNQHSMVSVSTPIADIYEQEKDEDGFLYMVYASQETFGF 132
                                    15        25        35        45        55        65        75        85        95       105       115       125

Chain C from PDB  Type:PROTEIN  Length:127
                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.............eeeee...hhhhhhhhhhhhhh.......eeee..........hhhhhhhhhh.....eeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dpr C   6 EWVNVGSPSDRPFKQRRSFADRCKEVQQIRDQHPSKIPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELVKIIRRRLQLNPTQAFFLLVNQHSMVSVSTPIADIYEQEKDEDGFLYMVYASQETFGF 132
                                    15        25        35        45        55        65        75        85        95       105       115       125

Chain D from PDB  Type:PROTEIN  Length:124
                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.............eeeee...hhhhhhhhhhhhh........eee....hhhhh..hhhhhhhhhh.....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dpr D   6 EWVNVGSPSDRPFKQRRSFADRCKEVQQIRDQHPSKIPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELVKIIRRRLQLNPTQAFFLLVNQHSMVSVSTPIADIYEQEKDEDGFLYMVYASQET 129
                                    15        25        35        45        55        65        75        85        95       105       115       125

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 5DPR)

(no "CATH Domain" information available for 5DPR)

(no "Pfam Domain" information available for 5DPR)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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(no "Ligands, Modified Residues, Ions" information available for 5dpr)

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	Cis Peptide Bonds
		Gly A:11 - Ser A:12	[ RasMol ]
		Gly C:11 - Ser C:12	[ RasMol ]
		Pro C:13 - Ser C:14	[ RasMol ]
		Ser B:14 - Asp B:15	[ RasMol ]
		Ser C:101 - Val C:102	[ RasMol ]
		Ser D:12 - Pro D:13	[ RasMol ]

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	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]
		Biological Unit 4	[ Jena3D ]

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	PKHM1_HUMAN \| Q9Y4G2
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		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	MLP3A_HUMAN \| Q9H492	:	3eci 3wal 3wan 4zdv 5cx3
	PKHM1_HUMAN \| Q9Y4G2	:	5dps 5dpt 5dpw

3x0w	3X0W CONTAINS SAME PROTEIN (PLEKHM1) COMPLEXED WITH LC3B
5dps	PLEKHM1 LIR-FUSED HUMAN GABARAP_2-117
5dpt	PLEKHM1 LIR-FUSED HUMAN GABARAPL1_2-117
5dpw	PLEKHM1 LIR-FUSED HUMAN LC3C_8-125

Description

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Ligands, Modified Residues, Ions (0, 0)

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Cis Peptide Bonds (6, 6)

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Exons (0, 0)

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SCOP Domains (0, 0)

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Gene Ontology (29, 32)

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