Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1XX1

Structural basis for ion-coordination and the catalytic mechanism of sphingomyelinases D

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0005576	cellular_component	extracellular region
A	0006629	biological_process	lipid metabolic process
A	0008081	molecular_function	phosphoric diester hydrolase activity
A	0016042	biological_process	lipid catabolic process
A	0016829	molecular_function	lyase activity
A	0031640	biological_process	killing of cells of another organism
A	0035821	biological_process	modulation of process of another organism
A	0046872	molecular_function	metal ion binding
A	0090729	molecular_function	toxin activity
B	0005576	cellular_component	extracellular region
B	0006629	biological_process	lipid metabolic process
B	0008081	molecular_function	phosphoric diester hydrolase activity
B	0016042	biological_process	lipid catabolic process
B	0016829	molecular_function	lyase activity
B	0031640	biological_process	killing of cells of another organism
B	0035821	biological_process	modulation of process of another organism
B	0046872	molecular_function	metal ion binding
B	0090729	molecular_function	toxin activity
C	0005576	cellular_component	extracellular region
C	0006629	biological_process	lipid metabolic process
C	0008081	molecular_function	phosphoric diester hydrolase activity
C	0016042	biological_process	lipid catabolic process
C	0016829	molecular_function	lyase activity
C	0031640	biological_process	killing of cells of another organism
C	0035821	biological_process	modulation of process of another organism
C	0046872	molecular_function	metal ion binding
C	0090729	molecular_function	toxin activity
D	0005576	cellular_component	extracellular region
D	0006629	biological_process	lipid metabolic process
D	0008081	molecular_function	phosphoric diester hydrolase activity
D	0016042	biological_process	lipid catabolic process
D	0016829	molecular_function	lyase activity
D	0031640	biological_process	killing of cells of another organism
D	0035821	biological_process	modulation of process of another organism
D	0046872	molecular_function	metal ion binding
D	0090729	molecular_function	toxin activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SO4 A 3001

Chain	Residue
A	HIS12
A	HIS47
A	LEU198
A	TRP230
A	MG9001
A	HOH9102
A	HOH9251
A	HOH9252
B	PRO50

site_id	AC2
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SO4 B 3002

Chain	Residue
A	PRO50
B	HIS12
B	HIS47
B	LEU198
B	TRP230
B	MG9002
B	HOH9104
B	HOH9256
B	HOH9259

site_id	AC3
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 C 3003

Chain	Residue
C	HIS12
C	HIS47
C	LEU198
C	TRP230
C	HOH9046
C	HOH9195
C	HOH9230
D	PRO50

site_id	AC4
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SO4 D 3004

Chain	Residue
C	PRO50
D	HIS12
D	HIS47
D	LEU198
D	TRP230
D	HOH9110
D	HOH9133
D	HOH9156
D	HOH9198

site_id	AC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 A 4001

Chain	Residue
A	ARG4
A	HOH9045
A	HOH9172
D	VAL65
D	LYS68
D	EPE2004

site_id	AC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 B 4002

Chain	Residue
B	ARG4
B	HOH9094
B	HOH9151
C	VAL65
C	LYS68
C	EPE2003

site_id	AC7
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 C 4003

Chain	Residue
C	ALA1
C	ASP2
C	ARG4
D	ALA1
D	ASP2
D	ASN3
D	ARG4
D	ARG271

site_id	AC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 A 5001

Chain	Residue
A	GLY39
A	SER40
A	GLN101
A	HOH9015
A	HOH9210
B	HOH9146

site_id	AC9
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 B 5002

Chain	Residue
B	GLY39
B	SER40
B	GLN101
B	HOH9111
B	HOH9134
B	HOH9181
B	HOH9228

site_id	BC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 C 5003

Chain	Residue
C	GLY39
C	SER40
C	GLN101
C	HOH9100

site_id	BC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 D 5004

Chain	Residue
D	GLY39
D	SER40
D	GLN101
D	HOH9101

site_id	BC3
Number of Residues	10
Details	BINDING SITE FOR RESIDUE SO4 A 6001

Chain	Residue
A	GLN19
A	ARG55
A	ASP56
A	HOH9009
A	HOH9023
A	HOH9180
A	HOH9243
C	LYS234
C	VAL235
C	HOH9045

site_id	BC4
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SO4 B 6002

Chain	Residue
B	GLN19
B	ARG55
B	ASP56
B	HOH9012
B	HOH9087
B	HOH9229
D	LYS234
D	VAL235
D	HOH9088

site_id	BC5
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SO4 C 6003

Chain	Residue
C	ARG55
C	ASP56
C	HOH9009
C	HOH9019
C	HOH9057
A	LYS234
A	VAL235
A	HOH9161
C	GLN19

site_id	BC6
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SO4 D 6004

Chain	Residue
B	LYS234
B	VAL235
D	GLN19
D	ARG55
D	ASP56
D	HOH9007
D	HOH9009
D	HOH9061
D	HOH9127

site_id	BC7
Number of Residues	2
Details	BINDING SITE FOR RESIDUE SO4 A 7001

Chain	Residue
A	ARG103
A	ARG143

site_id	BC8
Number of Residues	2
Details	BINDING SITE FOR RESIDUE SO4 B 7002

Chain	Residue
B	ARG103
B	ARG143

site_id	BC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 C 7003

Chain	Residue
C	ARG103
C	ARG143
C	HOH9214

site_id	CC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 D 7004

Chain	Residue
D	ARG103
D	ARG143
D	HOH9144

site_id	CC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 A 8001

Chain	Residue
A	GLU159
A	HIS191
A	HOH9144
A	HOH9146
A	HOH9213

site_id	CC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 B 8002

Chain	Residue
B	GLU159
B	HIS191
B	HOH9052
B	HOH9082
B	HOH9119
B	HOH9133
B	HOH9176

site_id	CC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 C 8003

Chain	Residue
C	GLU159
C	HIS191
C	HOH9071
C	HOH9106
C	HOH9167

site_id	CC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 D 8004

Chain	Residue
D	GLU159
D	HIS191
D	HOH9055
D	HOH9163
D	HOH9186
D	HOH9194

site_id	CC6
Number of Residues	7
Details	BINDING SITE FOR RESIDUE MG A 9001

Chain	Residue
A	GLU32
A	ASP34
A	ASP91
A	SO43001
A	HOH9245
A	HOH9251
A	HOH9252

site_id	CC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE MG B 9002

Chain	Residue
B	GLU32
B	ASP34
B	ASP91
B	SO43002
B	HOH9256
B	HOH9259
B	HOH9274

site_id	CC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG C 9003

Chain	Residue
C	GLU32
C	ASP34
C	ASP91
C	HOH9016
C	HOH9195
C	HOH9230

site_id	CC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG D 9004

Chain	Residue
D	GLU32
D	ASP34
D	ASP91
D	HOH9110
D	HOH9179
D	HOH9198

site_id	DC1
Number of Residues	10
Details	BINDING SITE FOR RESIDUE EPE A 2001

Chain	Residue
A	ALA16
A	ARG59
A	TRP60
A	GLU61
A	TYR62
A	VAL65
A	HOH9052
A	HOH9197
A	HOH9242
B	HOH9154

site_id	DC2
Number of Residues	13
Details	BINDING SITE FOR RESIDUE EPE C 2003

Chain	Residue
B	ARG4
B	ASN267
B	ASP268
B	SO44002
B	HOH9197
C	ALA16
C	ARG59
C	TRP60
C	GLU61
C	VAL65
C	HOH9090
C	HOH9184
C	HOH9219

site_id	DC3
Number of Residues	12
Details	BINDING SITE FOR RESIDUE EPE D 2004

Chain	Residue
A	ARG4
A	ASN267
A	ASP268
A	SO44001
D	ALA16
D	ARG59
D	TRP60
D	GLU61
D	VAL65
D	HOH9040
D	HOH9154
D	HOH9205

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	Active site: {"evidences":[{"source":"PubMed","id":"15654080","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	4
Details	Active site: {"description":"Nucleophile","evidences":[{"source":"PubMed","id":"15654080","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	12
Details	Binding site: {"evidences":[{"source":"PubMed","id":"15654080","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16480957","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1XX1","evidenceCode":"ECO:0000312"},{"source":"PDB","id":"2F9R","evidenceCode":"ECO:0000312"}]}

Chain

Residue

Details

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	11
Details	M-CSA 242

Chain	Residue	Details
A	HIS12	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
A	ASP233	activator, hydrogen bond acceptor
A	ASN252	activator, hydrogen bond acceptor, hydrogen bond donor
A	GLU32	metal ligand
A	ASP34	attractive charge-charge interaction, electrostatic stabiliser, hydrogen bond acceptor, metal ligand
A	HIS47	covalently attached, hydrogen bond donor, nucleofuge, nucleophile
A	GLY48	activator, electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor
A	ASP52	activator, hydrogen bond acceptor
A	ASP91	metal ligand
A	LYS93	attractive charge-charge interaction, electrostatic stabiliser, hydrogen bond donor
A	TRP230	electrostatic stabiliser, hydrogen bond donor

site_id	MCSA2
Number of Residues	11
Details	M-CSA 242

Chain	Residue	Details
B	HIS12	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
B	ASP233	activator, hydrogen bond acceptor
B	ASN252	activator, hydrogen bond acceptor, hydrogen bond donor
B	GLU32	metal ligand
B	ASP34	attractive charge-charge interaction, electrostatic stabiliser, hydrogen bond acceptor, metal ligand
B	HIS47	covalently attached, hydrogen bond donor, nucleofuge, nucleophile
B	GLY48	activator, electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor
B	ASP52	activator, hydrogen bond acceptor
B	ASP91	metal ligand
B	LYS93	attractive charge-charge interaction, electrostatic stabiliser, hydrogen bond donor
B	TRP230	electrostatic stabiliser, hydrogen bond donor

site_id	MCSA3
Number of Residues	11
Details	M-CSA 242

Chain	Residue	Details
C	HIS12	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
C	ASP233	activator, hydrogen bond acceptor
C	ASN252	activator, hydrogen bond acceptor, hydrogen bond donor
C	GLU32	metal ligand
C	ASP34	attractive charge-charge interaction, electrostatic stabiliser, hydrogen bond acceptor, metal ligand
C	HIS47	covalently attached, hydrogen bond donor, nucleofuge, nucleophile
C	GLY48	activator, electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor
C	ASP52	activator, hydrogen bond acceptor
C	ASP91	metal ligand
C	LYS93	attractive charge-charge interaction, electrostatic stabiliser, hydrogen bond donor
C	TRP230	electrostatic stabiliser, hydrogen bond donor

site_id	MCSA4
Number of Residues	11
Details	M-CSA 242

Chain	Residue	Details
D	HIS12	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
D	ASP233	activator, hydrogen bond acceptor
D	ASN252	activator, hydrogen bond acceptor, hydrogen bond donor
D	GLU32	metal ligand
D	ASP34	attractive charge-charge interaction, electrostatic stabiliser, hydrogen bond acceptor, metal ligand
D	HIS47	covalently attached, hydrogen bond donor, nucleofuge, nucleophile
D	GLY48	activator, electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor
D	ASP52	activator, hydrogen bond acceptor
D	ASP91	metal ligand
D	LYS93	attractive charge-charge interaction, electrostatic stabiliser, hydrogen bond donor
D	TRP230	electrostatic stabiliser, hydrogen bond donor

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