Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3A9C

Crystal structure of ribose-1,5-bisphosphate isomerase from Thermococcus kodakaraensis KOD1 in complex with ribulose-1,5-bisphosphate

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0016853	molecular_function	isomerase activity
A	0019323	biological_process	pentose catabolic process
A	0019509	biological_process	L-methionine salvage from methylthioadenosine
A	0043917	molecular_function	ribose 1,5-bisphosphate isomerase activity
A	0044237	biological_process	cellular metabolic process
A	0044249	biological_process	cellular biosynthetic process
A	0046523	molecular_function	S-methyl-5-thioribose-1-phosphate isomerase activity
B	0016853	molecular_function	isomerase activity
B	0019323	biological_process	pentose catabolic process
B	0019509	biological_process	L-methionine salvage from methylthioadenosine
B	0043917	molecular_function	ribose 1,5-bisphosphate isomerase activity
B	0044237	biological_process	cellular metabolic process
B	0044249	biological_process	cellular biosynthetic process
B	0046523	molecular_function	S-methyl-5-thioribose-1-phosphate isomerase activity
C	0016853	molecular_function	isomerase activity
C	0019323	biological_process	pentose catabolic process
C	0019509	biological_process	L-methionine salvage from methylthioadenosine
C	0043917	molecular_function	ribose 1,5-bisphosphate isomerase activity
C	0044237	biological_process	cellular metabolic process
C	0044249	biological_process	cellular biosynthetic process
C	0046523	molecular_function	S-methyl-5-thioribose-1-phosphate isomerase activity
D	0016853	molecular_function	isomerase activity
D	0019323	biological_process	pentose catabolic process
D	0019509	biological_process	L-methionine salvage from methylthioadenosine
D	0043917	molecular_function	ribose 1,5-bisphosphate isomerase activity
D	0044237	biological_process	cellular metabolic process
D	0044249	biological_process	cellular biosynthetic process
D	0046523	molecular_function	S-methyl-5-thioribose-1-phosphate isomerase activity
E	0016853	molecular_function	isomerase activity
E	0019323	biological_process	pentose catabolic process
E	0019509	biological_process	L-methionine salvage from methylthioadenosine
E	0043917	molecular_function	ribose 1,5-bisphosphate isomerase activity
E	0044237	biological_process	cellular metabolic process
E	0044249	biological_process	cellular biosynthetic process
E	0046523	molecular_function	S-methyl-5-thioribose-1-phosphate isomerase activity
F	0016853	molecular_function	isomerase activity
F	0019323	biological_process	pentose catabolic process
F	0019509	biological_process	L-methionine salvage from methylthioadenosine
F	0043917	molecular_function	ribose 1,5-bisphosphate isomerase activity
F	0044237	biological_process	cellular metabolic process
F	0044249	biological_process	cellular biosynthetic process
F	0046523	molecular_function	S-methyl-5-thioribose-1-phosphate isomerase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	11
Details	BINDING SITE FOR RESIDUE RUB A 401

Chain	Residue
A	CSD133
A	HOH601
A	HOH614
A	SER135
A	LYS136
A	ALA137
A	ALA201
A	ASN212
A	LYS213
A	LYS238
A	ARG254

site_id	AC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE PEG A 402

Chain	Residue
A	LYS224
A	VAL228
A	GLU285
A	ASP288

site_id	AC3
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MG A 411

Chain	Residue
A	ASP304
E	ASP304

site_id	AC4
Number of Residues	13
Details	BINDING SITE FOR RESIDUE RUB B 401

Chain	Residue
B	CSD133
B	SER135
B	LYS136
B	ALA137
B	ALA201
B	ASP202
B	ASN212
B	LYS213
B	LYS238
B	ARG254
B	HOH601
B	HOH603
B	HOH615

site_id	AC5
Number of Residues	7
Details	BINDING SITE FOR RESIDUE PEG B 402

Chain	Residue
B	ALA223
B	LYS224
B	ARG227
B	VAL228
B	THR230
B	TYR286
B	ASP288

site_id	AC6
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MG B 411

Chain	Residue
B	ASP304
D	ASP304

site_id	AC7
Number of Residues	12
Details	BINDING SITE FOR RESIDUE RUB C 401

Chain	Residue
C	CSD133
C	SER135
C	LYS136
C	ALA137
C	GLN164
C	ALA201
C	ASN212
C	LYS213
C	LYS238
C	ARG254
C	HOH601
C	HOH609

site_id	AC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE PEG C 402

Chain	Residue
C	LYS224
C	VAL228
C	GLU285
C	TYR286
C	ASP288

site_id	AC9
Number of Residues	13
Details	BINDING SITE FOR RESIDUE RUB D 401

Chain	Residue
D	CSD133
D	SER135
D	LYS136
D	ALA137
D	GLN164
D	ALA201
D	ASN212
D	LYS213
D	LYS238
D	ARG254
D	HOH601
D	HOH620
D	HOH627

site_id	BC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE PEG D 402

Chain	Residue
D	LYS224
D	ARG227
D	VAL228
D	TYR286
D	ASP288
D	HOH619

site_id	BC2
Number of Residues	12
Details	BINDING SITE FOR RESIDUE RUB E 401

Chain	Residue
E	CSD133
E	SER135
E	LYS136
E	ALA137
E	GLN164
E	ALA201
E	ASN212
E	LYS213
E	LYS238
E	ARG254
E	HOH601
E	HOH618

site_id	BC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE PEG E 402

Chain	Residue
E	LYS224
E	ARG227
E	VAL228
E	TRP229
E	ASP288

site_id	BC4
Number of Residues	11
Details	BINDING SITE FOR RESIDUE RUB F 401

Chain	Residue
F	LYS238
F	ARG254
F	HOH601
F	HOH633
F	CSD133
F	SER135
F	LYS136
F	ALA137
F	LYS162
F	ASN212
F	LYS213

site_id	BC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE PEG F 402

Chain	Residue
F	LYS224
F	ARG227
F	VAL228
F	THR230
F	ASP288
F	HOH637

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	6
Details	ACT_SITE: Proton acceptor => ECO:0000255\|HAMAP-Rule:MF_02230, ECO:0000269\|PubMed:22511789

Chain	Residue	Details
A	CSD133
B	CSD133
C	CSD133
D	CSD133
E	CSD133
F	CSD133

site_id	SWS_FT_FI2
Number of Residues	6
Details	ACT_SITE: Proton donor => ECO:0000255\|HAMAP-Rule:MF_02230, ECO:0000269\|PubMed:22511789

Chain	Residue	Details
A	ASP202
B	ASP202
C	ASP202
D	ASP202
E	ASP202
F	ASP202

site_id	SWS_FT_FI3
Number of Residues	18
Details	BINDING: BINDING => ECO:0000255\|HAMAP-Rule:MF_02230

Chain	Residue	Details
A	ARG20
D	ARG20
D	SER135
D	ASN212
E	ARG20
E	SER135
E	ASN212
F	ARG20
F	SER135
F	ASN212
A	SER135
A	ASN212
B	ARG20
B	SER135
B	ASN212
C	ARG20
C	SER135
C	ASN212

site_id	SWS_FT_FI4
Number of Residues	12
Details	BINDING: BINDING => ECO:0000255\|HAMAP-Rule:MF_02230, ECO:0000269\|PubMed:22511789

Chain	Residue	Details
A	ARG63
E	LYS238
F	ARG63
F	LYS238
A	LYS238
B	ARG63
B	LYS238
C	ARG63
C	LYS238
D	ARG63
D	LYS238
E	ARG63

site_id	SWS_FT_FI5
Number of Residues	6
Details	SITE: Plays a key role in hexamerization

Chain	Residue	Details
A	ARG227
B	ARG227
C	ARG227
D	ARG227
E	ARG227
F	ARG227

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