Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5CAW

Structure of Pediculus humanus Parkin bound to phospho-ubiquitin

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004842	molecular_function	ubiquitin-protein transferase activity
A	0005739	cellular_component	mitochondrion
A	0005829	cellular_component	cytosol
A	0008270	molecular_function	zinc ion binding
A	0016567	biological_process	protein ubiquitination
C	0004842	molecular_function	ubiquitin-protein transferase activity
C	0005739	cellular_component	mitochondrion
C	0005829	cellular_component	cytosol
C	0008270	molecular_function	zinc ion binding
C	0016567	biological_process	protein ubiquitination

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	binding site for residue ZN A 1001

Chain	Residue
A	CYS151
A	CYS155
A	CYS213
A	HIS216

site_id	AC2
Number of Residues	4
Details	binding site for residue ZN A 1002

Chain	Residue
A	CYS167
A	CYS170
A	CYS197
A	CYS202

site_id	AC3
Number of Residues	4
Details	binding site for residue ZN A 1003

Chain	Residue
A	CYS243
A	CYS262
A	CYS265
A	CYS240

site_id	AC4
Number of Residues	4
Details	binding site for residue ZN A 1004

Chain	Residue
A	CYS255
A	HIS259
A	CYS291
A	CYS295

site_id	AC5
Number of Residues	4
Details	binding site for residue ZN A 1005

Chain	Residue
A	CYS334
A	CYS339
A	CYS354
A	CYS356

site_id	AC6
Number of Residues	4
Details	binding site for residue ZN A 1006

Chain	Residue
A	CYS361
A	CYS364
A	HIS369
A	CYS373

site_id	AC7
Number of Residues	4
Details	binding site for residue ZN A 1007

Chain	Residue
A	CYS415
A	CYS418
A	CYS433
A	CYS438

site_id	AC8
Number of Residues	4
Details	binding site for residue ZN A 1008

Chain	Residue
A	CYS443
A	CYS446
A	CYS454
A	HIS458

site_id	AC9
Number of Residues	4
Details	binding site for residue SO4 A 1009

Chain	Residue
A	SER183
A	TRP184
A	ARG258
A	HOH1104

site_id	AD1
Number of Residues	4
Details	binding site for residue ZN C 1001

Chain	Residue
C	CYS151
C	CYS155
C	CYS213
C	HIS216

site_id	AD2
Number of Residues	4
Details	binding site for residue ZN C 1002

Chain	Residue
C	CYS167
C	CYS170
C	CYS197
C	CYS202

site_id	AD3
Number of Residues	4
Details	binding site for residue ZN C 1003

Chain	Residue
C	CYS240
C	CYS243
C	CYS262
C	CYS265

site_id	AD4
Number of Residues	4
Details	binding site for residue ZN C 1004

Chain	Residue
C	CYS255
C	HIS259
C	CYS291
C	CYS295

site_id	AD5
Number of Residues	4
Details	binding site for residue ZN C 1005

Chain	Residue
C	CYS334
C	CYS339
C	CYS354
C	CYS356

site_id	AD6
Number of Residues	4
Details	binding site for residue ZN C 1006

Chain	Residue
C	CYS361
C	CYS364
C	HIS369
C	CYS373

site_id	AD7
Number of Residues	4
Details	binding site for residue ZN C 1007

Chain	Residue
C	CYS415
C	CYS418
C	CYS433
C	CYS438

site_id	AD8
Number of Residues	4
Details	binding site for residue ZN C 1008

Chain	Residue
C	CYS443
C	CYS446
C	CYS454
C	HIS458

site_id	AD9
Number of Residues	3
Details	binding site for residue SO4 C 1009

Chain	Residue
C	TRP184
C	LYS232
C	ARG258

site_id	AE1
Number of Residues	8
Details	binding site for residue SO4 C 1010

Chain	Residue
A	HIS441
A	PRO449
C	GLY195
C	VAL196
C	CYS197
C	CYS202
C	GLU203
C	GLY204

site_id	AE2
Number of Residues	2
Details	binding site for residue SO4 C 1011

Chain	Residue
C	THR310
C	ASP311

site_id	AE3
Number of Residues	3
Details	binding site for residue SO4 D 101

Chain	Residue
D	ARG42
D	ARG72
D	ARG74

site_id	AE4
Number of Residues	4
Details	binding site for Di-peptide GLY D 75 and 3CN D 76

Chain	Residue
C	ASP346
C	CYS349
C	ARG351
D	ARG74

Functional Information from PROSITE/UniProt

site_id	PS00299
Number of Residues	26
Details	UBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGkqleD

Chain	Residue	Details
B	LYS27-ASP52

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	SITE: Interacts with activating enzyme

Chain	Residue	Details
B	ARG54
B	ARG72
D	ARG54
D	ARG72

site_id	SWS_FT_FI2
Number of Residues	2
Details	SITE: Essential for function

Chain	Residue	Details
B	HIS68
D	HIS68

site_id	SWS_FT_FI3
Number of Residues	2
Details	MOD_RES: Phosphoserine; by PINK1 => ECO:0000269\|PubMed:24660806, ECO:0000269\|PubMed:24751536, ECO:0000269\|PubMed:24784582, ECO:0000269\|PubMed:25527291

Chain	Residue	Details
B	SEP65
D	SEP65

site_id	SWS_FT_FI4
Number of Residues	2
Details	MOD_RES: (Microbial infection) ADP-ribosylthreonine => ECO:0000269\|PubMed:32330457

Chain	Residue	Details
B	THR66
D	THR66

site_id	SWS_FT_FI5
Number of Residues	2
Details	MOD_RES: ADP-ribosylglycine => ECO:0000269\|PubMed:28525742

Chain	Residue	Details
B	3CN76
D	3CN76

site_id	SWS_FT_FI6
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269\|PubMed:16443603

Chain	Residue	Details
B	LYS6
D	LYS6

site_id	SWS_FT_FI7
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)

Chain	Residue	Details
A	CYS151
A	CYS446
A	CYS454
A	HIS458
C	CYS151
C	CYS155
C	CYS167
C	CYS170
C	CYS197
C	CYS202
C	CYS213
B	3CN76
C	HIS216
C	CYS443
C	CYS446
C	CYS454
C	HIS458
A	CYS167
D	3CN76
A	CYS197
A	CYS202
A	CYS213
A	HIS216
A	CYS443

site_id	SWS_FT_FI8
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269\|PubMed:16443603, ECO:0000269\|PubMed:16543144

Chain	Residue	Details
B	LYS11
A	CYS339
A	CYS354
A	CYS356
A	CYS361
A	CYS364
A	HIS369
A	CYS373
A	CYS415
A	CYS418
A	CYS433
B	LYS48
A	CYS438
C	CYS240
C	CYS243
C	CYS255
C	HIS259
C	CYS262
C	CYS265
C	CYS291
C	CYS295
C	CYS334
D	LYS11
C	CYS339
C	CYS354
C	CYS356
C	CYS361
C	CYS364
C	HIS369
C	CYS373
C	CYS415
C	CYS418
C	CYS433
D	LYS48
C	CYS438
A	CYS262
A	CYS265
A	CYS291
A	CYS295
A	CYS334

site_id	SWS_FT_FI9
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000305\|PubMed:15466860

Chain	Residue	Details
B	LYS27
D	LYS27
A	TYR314
C	HIS304
C	ARG307
C	TYR314

site_id	SWS_FT_FI10
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269\|PubMed:16543144, ECO:0000269\|PubMed:25752573, ECO:0000269\|PubMed:25752577, ECO:0000269\|PubMed:34239127

Chain	Residue	Details
B	LYS29
D	LYS29

site_id	SWS_FT_FI11
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269\|PubMed:25752577

Chain	Residue	Details
B	LYS33
D	LYS33

site_id	SWS_FT_FI12
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269\|PubMed:16543144, ECO:0000269\|PubMed:18719106

Chain	Residue	Details
B	LYS63
D	LYS63

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)