Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3WQP

Crystal structure of Rubisco T289D mutant from Thermococcus kodakarensis

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000287	molecular_function	magnesium ion binding
A	0006196	biological_process	AMP catabolic process
A	0015977	biological_process	carbon fixation
A	0016491	molecular_function	oxidoreductase activity
A	0016829	molecular_function	lyase activity
A	0016984	molecular_function	ribulose-bisphosphate carboxylase activity
A	0046872	molecular_function	metal ion binding
B	0000287	molecular_function	magnesium ion binding
B	0006196	biological_process	AMP catabolic process
B	0015977	biological_process	carbon fixation
B	0016491	molecular_function	oxidoreductase activity
B	0016829	molecular_function	lyase activity
B	0016984	molecular_function	ribulose-bisphosphate carboxylase activity
B	0046872	molecular_function	metal ion binding
C	0000287	molecular_function	magnesium ion binding
C	0006196	biological_process	AMP catabolic process
C	0015977	biological_process	carbon fixation
C	0016491	molecular_function	oxidoreductase activity
C	0016829	molecular_function	lyase activity
C	0016984	molecular_function	ribulose-bisphosphate carboxylase activity
C	0046872	molecular_function	metal ion binding
D	0000287	molecular_function	magnesium ion binding
D	0006196	biological_process	AMP catabolic process
D	0015977	biological_process	carbon fixation
D	0016491	molecular_function	oxidoreductase activity
D	0016829	molecular_function	lyase activity
D	0016984	molecular_function	ribulose-bisphosphate carboxylase activity
D	0046872	molecular_function	metal ion binding
E	0000287	molecular_function	magnesium ion binding
E	0006196	biological_process	AMP catabolic process
E	0015977	biological_process	carbon fixation
E	0016491	molecular_function	oxidoreductase activity
E	0016829	molecular_function	lyase activity
E	0016984	molecular_function	ribulose-bisphosphate carboxylase activity
E	0046872	molecular_function	metal ion binding
F	0000287	molecular_function	magnesium ion binding
F	0006196	biological_process	AMP catabolic process
F	0015977	biological_process	carbon fixation
F	0016491	molecular_function	oxidoreductase activity
F	0016829	molecular_function	lyase activity
F	0016984	molecular_function	ribulose-bisphosphate carboxylase activity
F	0046872	molecular_function	metal ion binding
G	0000287	molecular_function	magnesium ion binding
G	0006196	biological_process	AMP catabolic process
G	0015977	biological_process	carbon fixation
G	0016491	molecular_function	oxidoreductase activity
G	0016829	molecular_function	lyase activity
G	0016984	molecular_function	ribulose-bisphosphate carboxylase activity
G	0046872	molecular_function	metal ion binding
H	0000287	molecular_function	magnesium ion binding
H	0006196	biological_process	AMP catabolic process
H	0015977	biological_process	carbon fixation
H	0016491	molecular_function	oxidoreductase activity
H	0016829	molecular_function	lyase activity
H	0016984	molecular_function	ribulose-bisphosphate carboxylase activity
H	0046872	molecular_function	metal ion binding
I	0000287	molecular_function	magnesium ion binding
I	0006196	biological_process	AMP catabolic process
I	0015977	biological_process	carbon fixation
I	0016491	molecular_function	oxidoreductase activity
I	0016829	molecular_function	lyase activity
I	0016984	molecular_function	ribulose-bisphosphate carboxylase activity
I	0046872	molecular_function	metal ion binding
J	0000287	molecular_function	magnesium ion binding
J	0006196	biological_process	AMP catabolic process
J	0015977	biological_process	carbon fixation
J	0016491	molecular_function	oxidoreductase activity
J	0016829	molecular_function	lyase activity
J	0016984	molecular_function	ribulose-bisphosphate carboxylase activity
J	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MG A 501

Chain	Residue
A	KCX189
A	ASP191
A	GLU192
A	CAP502

site_id	AC2
Number of Residues	29
Details	BINDING SITE FOR RESIDUE CAP A 502

Chain	Residue
A	HIS281
A	ARG282
A	HIS314
A	LYS322
A	LEU323
A	SER367
A	GLY368
A	GLY369
A	GLN389
A	GLY391
A	GLY392
A	MG501
A	HOH625
A	HOH641
A	HOH645
A	HOH666
A	HOH703
A	HOH783
C	GLU49
C	THR54
C	TRP55
C	ASN111
C	HOH666
C	HOH778
A	LYS163
A	LYS165
A	KCX189
A	ASP191
A	GLU192

site_id	AC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO A 503

Chain	Residue
A	ASP214
A	LEU247
A	GLY248

site_id	AC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG B 501

Chain	Residue
B	LYS165
B	KCX189
B	ASP191
B	GLU192
B	CAP502

site_id	AC5
Number of Residues	27
Details	BINDING SITE FOR RESIDUE CAP B 502

Chain	Residue
B	GLU49
B	THR54
B	TRP55
B	ASN111
B	LYS163
B	LYS165
B	KCX189
B	ASP191
B	GLU192
B	HIS281
B	ARG282
B	HIS314
B	LYS322
B	LEU323
B	SER367
B	GLY368
B	GLY369
B	GLN389
B	GLY391
B	GLY392
B	MG501
B	HOH638
B	HOH681
B	HOH686
B	HOH725
B	HOH726
B	HOH727

site_id	AC6
Number of Residues	9
Details	BINDING SITE FOR RESIDUE EDO B 503

Chain	Residue
B	GLU97
B	ALA99
B	ASN100
B	LEU101
B	GLU135
B	PHE136
B	HOH667
B	HOH688
B	HOH708

site_id	AC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG C 501

Chain	Residue
A	ASN111
C	LYS165
C	KCX189
C	ASP191
C	GLU192
C	CAP502

site_id	AC8
Number of Residues	27
Details	BINDING SITE FOR RESIDUE CAP C 502

Chain	Residue
C	GLY368
C	GLY369
C	GLN389
C	GLY391
C	GLY392
C	MG501
C	HOH674
C	HOH684
C	HOH685
C	HOH754
C	HOH821
A	GLU49
A	TRP55
A	ASN111
A	HOH624
A	HOH686
C	LYS163
C	LYS165
C	KCX189
C	ASP191
C	GLU192
C	HIS281
C	ARG282
C	HIS314
C	LYS322
C	LEU323
C	SER367

site_id	AC9
Number of Residues	8
Details	BINDING SITE FOR RESIDUE EDO C 503

Chain	Residue
C	GLU97
C	ALA99
C	ASN100
C	LEU101
C	GLU135
C	PHE136
C	HOH665
C	HOH815

site_id	BC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG D 501

Chain	Residue
D	LYS163
D	KCX189
D	ASP191
D	GLU192
D	CAP502

site_id	BC2
Number of Residues	29
Details	BINDING SITE FOR RESIDUE CAP D 502

Chain	Residue
D	LYS163
D	LYS165
D	KCX189
D	ASP191
D	GLU192
D	HIS281
D	ARG282
D	HIS314
D	LYS322
D	LEU323
D	SER367
D	GLY368
D	GLY369
D	GLN389
D	GLY391
D	GLY392
D	MG501
D	HOH611
D	HOH619
D	HOH632
D	HOH650
D	HOH659
D	HOH828
E	GLU49
E	THR54
E	TRP55
E	ASN111
E	HOH660
E	HOH727

site_id	BC3
Number of Residues	9
Details	BINDING SITE FOR RESIDUE EDO D 503

Chain	Residue
D	GLU97
D	ALA99
D	ASN100
D	LEU101
D	LEU132
D	GLU135
D	PHE136
D	HOH655
D	HOH835

site_id	BC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG E 501

Chain	Residue
D	ASN111
E	KCX189
E	ASP191
E	GLU192
E	CAP502

site_id	BC5
Number of Residues	27
Details	BINDING SITE FOR RESIDUE CAP E 502

Chain	Residue
D	TRP55
D	ASN111
E	LYS163
E	LYS165
E	KCX189
E	ASP191
E	GLU192
E	HIS281
E	ARG282
E	HIS314
E	LYS322
E	LEU323
E	SER367
E	GLY368
E	GLY369
E	GLN389
E	GLY391
E	GLY392
E	MG501
E	HOH640
E	HOH659
E	HOH688
E	HOH708
E	HOH776
E	HOH781
E	HOH851
E	HOH852

site_id	BC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO E 503

Chain	Residue
D	GLU238
D	TYR266
E	GLU238

site_id	BC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MG F 501

Chain	Residue
F	KCX189
F	ASP191
F	GLU192
F	CAP502

site_id	BC8
Number of Residues	27
Details	BINDING SITE FOR RESIDUE CAP F 502

Chain	Residue
F	LYS163
F	LYS165
F	KCX189
F	ASP191
F	GLU192
F	HIS281
F	ARG282
F	HIS314
F	LYS322
F	LEU323
F	SER367
F	GLY368
F	GLY369
F	GLN389
F	GLY391
F	GLY392
F	MG501
F	HOH652
F	HOH663
F	HOH666
F	HOH692
F	HOH770
H	GLU49
H	THR54
H	TRP55
H	ASN111
H	HOH721

site_id	BC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG G 501

Chain	Residue
G	LYS165
G	KCX189
G	ASP191
G	GLU192
G	CAP502

site_id	CC1
Number of Residues	27
Details	BINDING SITE FOR RESIDUE CAP G 502

Chain	Residue
G	GLU49
G	TRP55
G	ASN111
G	LYS163
G	LYS165
G	KCX189
G	ASP191
G	GLU192
G	HIS281
G	ARG282
G	HIS314
G	LYS322
G	LEU323
G	SER367
G	GLY368
G	GLY369
G	GLN389
G	GLY391
G	GLY392
G	MG501
G	HOH622
G	HOH634
G	HOH668
G	HOH683
G	HOH699
G	HOH732
G	HOH733

site_id	CC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG H 501

Chain	Residue
H	LYS165
H	KCX189
H	ASP191
H	GLU192
H	CAP502

site_id	CC3
Number of Residues	26
Details	BINDING SITE FOR RESIDUE CAP H 502

Chain	Residue
F	GLU49
F	TRP55
F	ASN111
H	LYS163
H	LYS165
H	KCX189
H	ASP191
H	GLU192
H	HIS281
H	ARG282
H	HIS314
H	LYS322
H	LEU323
H	SER367
H	GLY368
H	GLY369
H	GLN389
H	GLY391
H	GLY392
H	MG501
H	HOH646
H	HOH664
H	HOH699
H	HOH748
H	HOH782
H	HOH783

site_id	CC4
Number of Residues	8
Details	BINDING SITE FOR RESIDUE EDO H 503

Chain	Residue
H	GLU97
H	ALA99
H	ASN100
H	LEU101
H	GLU135
H	PHE136
H	HOH651
H	HOH753

site_id	CC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO H 504

Chain	Residue
F	GLU238
H	GLU238
H	TYR266

site_id	CC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG I 501

Chain	Residue
I	LYS163
I	LYS165
I	KCX189
I	ASP191
I	GLU192
I	CAP502

site_id	CC7
Number of Residues	29
Details	BINDING SITE FOR RESIDUE CAP I 502

Chain	Residue
I	LYS163
I	LYS165
I	KCX189
I	ASP191
I	GLU192
I	HIS281
I	ARG282
I	HIS314
I	LYS322
I	LEU323
I	SER367
I	GLY368
I	GLY369
I	GLN389
I	GLY391
I	GLY392
I	MG501
I	HOH617
I	HOH621
I	HOH638
I	HOH672
I	HOH673
I	HOH676
I	HOH694
I	HOH759
J	GLU49
J	THR54
J	TRP55
J	ASN111

site_id	CC8
Number of Residues	8
Details	BINDING SITE FOR RESIDUE EDO I 503

Chain	Residue
I	GLU97
I	ALA99
I	ASN100
I	LEU101
I	GLU135
I	PHE136
I	HOH656
I	HOH811

site_id	CC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO I 504

Chain	Residue
I	GLU238
I	TYR266
J	GLU238
J	TYR266

site_id	DC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MG J 501

Chain	Residue
J	KCX189
J	ASP191
J	GLU192
J	CAP502

site_id	DC2
Number of Residues	29
Details	BINDING SITE FOR RESIDUE CAP J 502

Chain	Residue
I	GLU49
I	TRP55
I	ASN111
I	HOH631
I	HOH706
J	LYS163
J	LYS165
J	KCX189
J	ASP191
J	GLU192
J	HIS281
J	ARG282
J	HIS314
J	LYS322
J	LEU323
J	SER367
J	GLY368
J	GLY369
J	GLN389
J	GLY391
J	GLY392
J	MG501
J	HOH679
J	HOH706
J	HOH713
J	HOH718
J	HOH804
J	HOH835
J	HOH854

site_id	DC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO J 503

Chain	Residue
J	GLU97
J	ALA99
J	ASN100
J	LEU132
J	GLU135
J	PHE136

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	20
Details	ACT_SITE: Proton acceptor => ECO:0000255\|HAMAP-Rule:MF_01133

Chain	Residue	Details
A	LYS163
E	HIS281
F	LYS163
F	HIS281
G	LYS163
G	HIS281
H	LYS163
H	HIS281
I	LYS163
I	HIS281
J	LYS163
A	HIS281
J	HIS281
B	LYS163
B	HIS281
C	LYS163
C	HIS281
D	LYS163
D	HIS281
E	LYS163

site_id	SWS_FT_FI2
Number of Residues	50
Details	BINDING: BINDING => ECO:0000305

Chain	Residue	Details
A	LYS165
B	GLN389
C	LYS165
C	ARG282
C	HIS314
C	SER367
C	GLN389
D	LYS165
D	ARG282
D	HIS314
D	SER367
A	ARG282
D	GLN389
E	LYS165
E	ARG282
E	HIS314
E	SER367
E	GLN389
F	LYS165
F	ARG282
F	HIS314
F	SER367
A	HIS314
F	GLN389
G	LYS165
G	ARG282
G	HIS314
G	SER367
G	GLN389
H	LYS165
H	ARG282
H	HIS314
H	SER367
A	SER367
H	GLN389
I	LYS165
I	ARG282
I	HIS314
I	SER367
I	GLN389
J	LYS165
J	ARG282
J	HIS314
J	SER367
A	GLN389
J	GLN389
B	LYS165
B	ARG282
B	HIS314
B	SER367

site_id	SWS_FT_FI3
Number of Residues	10
Details	BINDING: via carbamate group => ECO:0000255\|HAMAP-Rule:MF_01133, ECO:0000269\|PubMed:20926376

Chain	Residue	Details
A	KCX189
J	KCX189
B	KCX189
C	KCX189
D	KCX189
E	KCX189
F	KCX189
G	KCX189
H	KCX189
I	KCX189

site_id	SWS_FT_FI4
Number of Residues	20
Details	BINDING: BINDING => ECO:0000255\|HAMAP-Rule:MF_01133, ECO:0000269\|PubMed:20926376

Chain	Residue	Details
A	ASP191
E	GLU192
F	ASP191
F	GLU192
G	ASP191
G	GLU192
H	ASP191
H	GLU192
I	ASP191
I	GLU192
J	ASP191
A	GLU192
J	GLU192
B	ASP191
B	GLU192
C	ASP191
C	GLU192
D	ASP191
D	GLU192
E	ASP191

site_id	SWS_FT_FI5
Number of Residues	10
Details	SITE: Transition state stabilizer => ECO:0000255\|HAMAP-Rule:MF_01133

Chain	Residue	Details
A	LYS322
J	LYS322
B	LYS322
C	LYS322
D	LYS322
E	LYS322
F	LYS322
G	LYS322
H	LYS322
I	LYS322

site_id	SWS_FT_FI6
Number of Residues	10
Details	MOD_RES: N6-carboxylysine => ECO:0000255\|HAMAP-Rule:MF_01133, ECO:0000269\|PubMed:20926376

Chain	Residue	Details
A	KCX189
J	KCX189
B	KCX189
C	KCX189
D	KCX189
E	KCX189
F	KCX189
G	KCX189
H	KCX189
I	KCX189

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