Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4L9Z

Crystal Structure of Rhodobacter sphaeroides malyl-CoA lyase in complex with magnesium, oxalate, and CoA

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000287	molecular_function	magnesium ion binding
A	0003824	molecular_function	catalytic activity
A	0006107	biological_process	oxaloacetate metabolic process
A	0016829	molecular_function	lyase activity
A	0043959	molecular_function	L-erythro-3-methylmalyl-CoA lyase activity
A	0046872	molecular_function	metal ion binding
A	0047777	molecular_function	(S)-citramalyl-CoA lyase activity
A	0050083	molecular_function	malyl-CoA lyase activity
B	0000287	molecular_function	magnesium ion binding
B	0003824	molecular_function	catalytic activity
B	0006107	biological_process	oxaloacetate metabolic process
B	0016829	molecular_function	lyase activity
B	0043959	molecular_function	L-erythro-3-methylmalyl-CoA lyase activity
B	0046872	molecular_function	metal ion binding
B	0047777	molecular_function	(S)-citramalyl-CoA lyase activity
B	0050083	molecular_function	malyl-CoA lyase activity
C	0000287	molecular_function	magnesium ion binding
C	0003824	molecular_function	catalytic activity
C	0006107	biological_process	oxaloacetate metabolic process
C	0016829	molecular_function	lyase activity
C	0043959	molecular_function	L-erythro-3-methylmalyl-CoA lyase activity
C	0046872	molecular_function	metal ion binding
C	0047777	molecular_function	(S)-citramalyl-CoA lyase activity
C	0050083	molecular_function	malyl-CoA lyase activity
D	0000287	molecular_function	magnesium ion binding
D	0003824	molecular_function	catalytic activity
D	0006107	biological_process	oxaloacetate metabolic process
D	0016829	molecular_function	lyase activity
D	0043959	molecular_function	L-erythro-3-methylmalyl-CoA lyase activity
D	0046872	molecular_function	metal ion binding
D	0047777	molecular_function	(S)-citramalyl-CoA lyase activity
D	0050083	molecular_function	malyl-CoA lyase activity
E	0000287	molecular_function	magnesium ion binding
E	0003824	molecular_function	catalytic activity
E	0006107	biological_process	oxaloacetate metabolic process
E	0016829	molecular_function	lyase activity
E	0043959	molecular_function	L-erythro-3-methylmalyl-CoA lyase activity
E	0046872	molecular_function	metal ion binding
E	0047777	molecular_function	(S)-citramalyl-CoA lyase activity
E	0050083	molecular_function	malyl-CoA lyase activity
F	0000287	molecular_function	magnesium ion binding
F	0003824	molecular_function	catalytic activity
F	0006107	biological_process	oxaloacetate metabolic process
F	0016829	molecular_function	lyase activity
F	0043959	molecular_function	L-erythro-3-methylmalyl-CoA lyase activity
F	0046872	molecular_function	metal ion binding
F	0047777	molecular_function	(S)-citramalyl-CoA lyase activity
F	0050083	molecular_function	malyl-CoA lyase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	19
Details	BINDING SITE FOR RESIDUE COA A 401

Chain	Residue
A	PHE19
A	HIS252
A	PRO253
A	OXL402
A	HOH513
A	HOH743
A	HOH799
A	HOH809
A	HOH844
A	HOH873
C	ASP299
A	GLY20
A	PRO21
A	LEU27
A	LYS30
A	MET31
A	SER46
A	ARG76
A	ILE251

site_id	AC2
Number of Residues	13
Details	BINDING SITE FOR RESIDUE OXL A 402

Chain	Residue
A	ARG76
A	GLU141
A	GLY165
A	ALA166
A	ALA167
A	ASP168
A	PRO223
A	TRP249
A	COA401
A	MG403
A	HOH505
A	HOH513
C	HOH609

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG A 403

Chain	Residue
A	GLU141
A	ASP168
A	OXL402
A	HOH502
A	HOH505

site_id	AC4
Number of Residues	21
Details	BINDING SITE FOR RESIDUE COA B 401

Chain	Residue
A	ASP299
B	PHE19
B	GLY20
B	PRO21
B	ARG24
B	LEU27
B	LYS30
B	MET31
B	ASP42
B	SER46
B	ARG76
B	TRP249
B	ILE251
B	HIS252
B	PRO253
B	OXL402
B	HOH523
B	HOH650
B	HOH743
B	HOH886
B	HOH911

site_id	AC5
Number of Residues	13
Details	BINDING SITE FOR RESIDUE OXL B 402

Chain	Residue
B	ARG76
B	GLU141
B	GLY165
B	ALA166
B	ALA167
B	ASP168
B	PRO223
B	TRP249
B	COA401
B	MG403
B	HOH504
B	HOH523
B	HOH894

site_id	AC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG B 403

Chain	Residue
B	GLU141
B	ASP168
B	OXL402
B	HOH502
B	HOH504

site_id	AC7
Number of Residues	18
Details	BINDING SITE FOR RESIDUE COA C 401

Chain	Residue
B	ASP299
C	PHE19
C	GLY20
C	PRO21
C	ARG24
C	LYS30
C	MET31
C	SER46
C	ARG76
C	ILE251
C	HIS252
C	PRO253
C	OXL402
C	HOH528
C	HOH587
C	HOH678
C	HOH811
C	HOH844

site_id	AC8
Number of Residues	12
Details	BINDING SITE FOR RESIDUE OXL C 402

Chain	Residue
C	ASP168
C	PRO223
C	COA401
C	MG403
C	HOH528
C	HOH714
C	HOH931
C	ARG76
C	GLU141
C	GLY165
C	ALA166
C	ALA167

site_id	AC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG C 403

Chain	Residue
C	GLU141
C	ASP168
C	OXL402
C	HOH504
C	HOH931

site_id	BC1
Number of Residues	20
Details	BINDING SITE FOR RESIDUE COA D 401

Chain	Residue
D	PHE19
D	GLY20
D	PRO21
D	ARG24
D	LEU27
D	LYS30
D	MET31
D	SER46
D	ARG76
D	ILE251
D	HIS252
D	PRO253
D	OXL402
D	HOH517
D	HOH771
D	HOH864
D	HOH904
D	HOH905
F	VAL292
F	ASP299

site_id	BC2
Number of Residues	13
Details	BINDING SITE FOR RESIDUE OXL D 402

Chain	Residue
D	ARG76
D	GLU141
D	GLY165
D	ALA166
D	ALA167
D	ASP168
D	PRO223
D	TRP249
D	COA401
D	MG403
D	HOH506
D	HOH517
F	HOH753

site_id	BC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG D 403

Chain	Residue
D	GLU141
D	ASP168
D	OXL402
D	HOH506
D	HOH507

site_id	BC4
Number of Residues	19
Details	BINDING SITE FOR RESIDUE COA E 401

Chain	Residue
D	ASP299
E	PHE19
E	GLY20
E	PRO21
E	ARG24
E	LEU27
E	LYS30
E	MET31
E	ASP42
E	SER46
E	ARG76
E	ILE251
E	HIS252
E	PRO253
E	OXL402
E	HOH549
E	HOH556
E	HOH592
E	HOH895

site_id	BC5
Number of Residues	14
Details	BINDING SITE FOR RESIDUE OXL E 402

Chain	Residue
E	ARG76
E	GLU141
E	GLY165
E	ALA166
E	ALA167
E	ASP168
E	PRO223
E	TRP249
E	COA401
E	MG403
E	HOH503
E	HOH505
E	HOH549
E	HOH691

site_id	BC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG E 403

Chain	Residue
E	GLU141
E	ASP168
E	OXL402
E	HOH503
E	HOH505

site_id	BC7
Number of Residues	16
Details	BINDING SITE FOR RESIDUE COA F 401

Chain	Residue
E	ASP299
F	PHE19
F	GLY20
F	PRO21
F	ARG24
F	LEU27
F	MET31
F	SER46
F	ARG76
F	ILE251
F	HIS252
F	PRO253
F	OXL402
F	HOH524
F	HOH873
F	HOH900

site_id	BC8
Number of Residues	13
Details	BINDING SITE FOR RESIDUE OXL F 402

Chain	Residue
F	ARG76
F	GLU141
F	GLY165
F	ALA166
F	ALA167
F	ASP168
F	PRO223
F	TRP249
F	COA401
F	MG403
F	HOH507
F	HOH524
F	HOH637

site_id	BC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG F 403

Chain	Residue
F	GLU141
F	ASP168
F	OXL402
F	HOH504
F	HOH507

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	12
Details	BINDING: BINDING => ECO:0000269\|PubMed:24206647, ECO:0007744\|PDB:4L9Y

Chain	Residue	Details
A	PHE19
A	ARG24
B	PHE19
B	ARG24
C	PHE19
C	ARG24
D	PHE19
D	ARG24
E	PHE19
E	ARG24
F	PHE19
F	ARG24

site_id	SWS_FT_FI2
Number of Residues	18
Details	BINDING: BINDING => ECO:0000269\|PubMed:24206647, ECO:0007744\|PDB:4L9Z

Chain	Residue	Details
C	LYS30
C	ALA167
C	ILE251
D	LYS30
D	ALA167
D	ILE251
E	LYS30
E	ALA167
E	ILE251
F	LYS30
F	ALA167
F	ILE251
A	LYS30
A	ALA167
A	ILE251
B	LYS30
B	ALA167
B	ILE251

site_id	SWS_FT_FI3
Number of Residues	18
Details	BINDING: BINDING => ECO:0000269\|PubMed:24206647, ECO:0007744\|PDB:4L9Y, ECO:0007744\|PDB:4L9Z

Chain	Residue	Details
C	ARG76
C	GLU141
C	ASP168
D	ARG76
D	GLU141
D	ASP168
E	ARG76
E	GLU141
E	ASP168
F	ARG76
F	GLU141
F	ASP168
A	ARG76
A	GLU141
A	ASP168
B	ARG76
B	GLU141
B	ASP168

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