Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1WDD

Crystal Structure of Activated Rice Rubisco Complexed with 2-Carboxyarabinitol-1,5-bisphosphate

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0000287	molecular_function	magnesium ion binding
A	0004497	molecular_function	monooxygenase activity
A	0009507	cellular_component	chloroplast
A	0009536	cellular_component	plastid
A	0009853	biological_process	photorespiration
A	0015977	biological_process	carbon fixation
A	0015979	biological_process	photosynthesis
A	0016491	molecular_function	oxidoreductase activity
A	0016829	molecular_function	lyase activity
A	0016984	molecular_function	ribulose-bisphosphate carboxylase activity
A	0019253	biological_process	reductive pentose-phosphate cycle
A	0046872	molecular_function	metal ion binding
E	0000166	molecular_function	nucleotide binding
E	0000287	molecular_function	magnesium ion binding
E	0004497	molecular_function	monooxygenase activity
E	0009507	cellular_component	chloroplast
E	0009536	cellular_component	plastid
E	0009853	biological_process	photorespiration
E	0015977	biological_process	carbon fixation
E	0015979	biological_process	photosynthesis
E	0016491	molecular_function	oxidoreductase activity
E	0016829	molecular_function	lyase activity
E	0016984	molecular_function	ribulose-bisphosphate carboxylase activity
E	0019253	biological_process	reductive pentose-phosphate cycle
E	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG A 1476

Chain	Residue
A	LYS177
A	KCX201
A	ASP203
A	GLU204
A	CAP1001

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG E 2476

Chain	Residue
E	CAP2001
E	LYS177
E	KCX201
E	ASP203
E	GLU204

site_id	AC3
Number of Residues	29
Details	BINDING SITE FOR RESIDUE CAP A 1001

Chain	Residue
A	THR173
A	LYS175
A	LYS177
A	KCX201
A	ASP203
A	GLU204
A	HIS294
A	ARG295
A	HIS327
A	LYS334
A	LEU335
A	SER379
A	GLY380
A	GLY381
A	GLY403
A	GLY404
A	MG1476
A	HOH3108
A	HOH3109
A	HOH3115
A	HOH3117
A	HOH3131
A	HOH3132
E	GLU60
E	THR65
E	TRP66
E	ASN123
E	HOH3028
E	HOH3038

site_id	AC4
Number of Residues	29
Details	BINDING SITE FOR RESIDUE CAP E 2001

Chain	Residue
A	GLU60
A	THR65
A	TRP66
A	ASN123
A	HOH3032
A	HOH3055
E	THR173
E	LYS175
E	LYS177
E	KCX201
E	ASP203
E	GLU204
E	HIS294
E	ARG295
E	HIS327
E	LYS334
E	LEU335
E	SER379
E	GLY380
E	GLY381
E	GLY403
E	GLY404
E	MG2476
E	HOH3020
E	HOH3044
E	HOH3045
E	HOH3046
E	HOH3130
E	HOH3131

site_id	AC5
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GOL A 3001

Chain	Residue
A	LYS32
A	PRO104
A	LEU105
A	ASP106
A	HOH3027
A	HOH3166
A	HOH3167
A	HOH3407
E	HOH3142

site_id	AC6
Number of Residues	10
Details	BINDING SITE FOR RESIDUE GOL E 3002

Chain	Residue
A	HOH3127
A	HOH3204
A	HOH3205
E	LYS32
E	PRO104
E	LEU105
E	ASP106
E	HOH3053
E	HOH3362
E	HOH3375

site_id	AC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL E 3003

Chain	Residue
A	LEU270
E	LEU270
E	MET297
E	HOH3035
E	HOH3036
E	HOH3037

site_id	AC8
Number of Residues	10
Details	BINDING SITE FOR RESIDUE GOL A 3004

Chain	Residue
A	THR68
A	GOL3010
A	HOH3021
A	HOH3036
A	GLY16
A	VAL17
A	LYS18
A	TYR20
A	THR65
A	THR67

site_id	AC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE GOL E 3005

Chain	Residue
E	GLU52
E	HOH3042
E	HOH3058

site_id	BC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL A 3006

Chain	Residue
A	GLU52
A	HOH3029
A	HOH3030
A	HOH3259
A	HOH3360

site_id	BC2
Number of Residues	10
Details	BINDING SITE FOR RESIDUE GOL W 3007

Chain	Residue
E	ASN163
E	ARG187
W	GLU43
W	ARG64
W	TYR65
W	TRP66
W	ARG99
W	GLN110
W	HOH536
W	HOH558

site_id	BC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL W 3008

Chain	Residue
W	GLN2
W	VAL3
W	TRP69
W	ALA92
W	HOH312
W	HOH669

site_id	BC4
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL E 3009

Chain	Residue
E	TYR226
E	GLN229
E	ALA230
E	HOH3366
W	VAL50
W	ASN54
W	ARG56
W	HOH555

site_id	BC5
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GOL A 3010

Chain	Residue
A	LYS18
A	THR23
A	THR68
A	ASP72
A	LEU77
A	GOL3004
A	GOL3012
A	HOH3038
A	HOH3327

site_id	BC6
Number of Residues	10
Details	BINDING SITE FOR RESIDUE GOL E 3011

Chain	Residue
E	GLY16
E	VAL17
E	LYS18
E	TYR20
E	THR65
E	THR67
E	THR68
E	HOH3026
E	HOH3049
E	HOH3304

site_id	BC7
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL A 3012

Chain	Residue
A	VAL11
A	PHE13
A	THR68
A	VAL69
A	TRP70
A	GLY73
A	GOL3010
W	PHE74

site_id	BC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL E 3013

Chain	Residue
E	THR68
E	VAL69
E	TRP70
E	HOH3183

site_id	BC9
Number of Residues	10
Details	BINDING SITE FOR RESIDUE GOL E 3014

Chain	Residue
E	ARG295
E	HIS298
E	PHE311
E	GLY329
E	GLU336
E	PHE345
E	HOH3128
E	HOH3133
E	HOH3172
E	HOH3300

site_id	CC1
Number of Residues	10
Details	BINDING SITE FOR RESIDUE GOL A 3015

Chain	Residue
A	ASN163
A	ARG187
A	HOH3303
S	GLU43
S	ARG64
S	TYR65
S	TRP66
S	ARG99
S	GLN110
S	HOH177

site_id	CC2
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GOL E 3016

Chain	Residue
A	HOH3263
E	ILE155
E	GLN156
E	ARG350
E	ASP351
E	ASP352
E	PRO372
E	GLY373
E	HOH3141

site_id	CC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL A 3017

Chain	Residue
A	THR23
A	LEU77
A	ASP78
A	LYS81
A	HOH3161

Functional Information from PROSITE/UniProt

site_id	PS00157
Number of Residues	9
Details	RUBISCO_LARGE Ribulose bisphosphate carboxylase large chain active site. GlDFtKdDE

Chain	Residue	Details
A	GLY196-GLU204

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	Active site: {"description":"Proton acceptor","evidences":[{"source":"HAMAP-Rule","id":"MF_01338","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	16
Details	Binding site: {"evidences":[{"source":"PubMed","id":"22609438","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3AXK","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	16
Details	Binding site: {"evidences":[{"source":"PubMed","id":"22609438","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1WDD","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	2
Details	Binding site: {"description":"in homodimeric partner","evidences":[{"source":"PubMed","id":"22609438","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1WDD","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3AXM","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	2
Details	Binding site: {"description":"via carbamate group","evidences":[{"source":"PubMed","id":"22609438","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1WDD","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3AXK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3AXM","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"22609438","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1WDD","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3AXK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3AXM","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PDB","id":"1WDD","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"PubMed","id":"22609438","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	2
Details	Site: {"description":"Transition state stabilizer"}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	2
Details	Modified residue: {"description":"N6-carboxylysine","evidences":[{"source":"PubMed","id":"22609438","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	8
Details	Region: {"description":"Interaction with large subunit"}

Chain

Residue

Details

Catalytic Information from CSA

site_id	CSA1
Number of Residues	5
Details	Annotated By Reference To The Literature 1rbl

Chain	Residue	Details
A	LYS175
A	HIS294
A	LYS177
A	ASP203
A	HIS327

site_id	CSA2
Number of Residues	5
Details	Annotated By Reference To The Literature 1rbl

Chain	Residue	Details
E	LYS175
E	HIS294
E	LYS177
E	ASP203
E	HIS327

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