Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1VKM

Crystal structure of an indigoidine synthase a (idga)-like protein (tm1464) from thermotoga maritima msb8 at 1.90 A resolution

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0001522	biological_process	pseudouridine synthesis
A	0004730	molecular_function	pseudouridylate synthase activity
A	0005737	cellular_component	cytoplasm
A	0016798	molecular_function	hydrolase activity, acting on glycosyl bonds
A	0016829	molecular_function	lyase activity
A	0046113	biological_process	nucleobase catabolic process
A	0046872	molecular_function	metal ion binding
B	0001522	biological_process	pseudouridine synthesis
B	0004730	molecular_function	pseudouridylate synthase activity
B	0005737	cellular_component	cytoplasm
B	0016798	molecular_function	hydrolase activity, acting on glycosyl bonds
B	0016829	molecular_function	lyase activity
B	0046113	biological_process	nucleobase catabolic process
B	0046872	molecular_function	metal ion binding
C	0001522	biological_process	pseudouridine synthesis
C	0004730	molecular_function	pseudouridylate synthase activity
C	0005737	cellular_component	cytoplasm
C	0016798	molecular_function	hydrolase activity, acting on glycosyl bonds
C	0016829	molecular_function	lyase activity
C	0046113	biological_process	nucleobase catabolic process
C	0046872	molecular_function	metal ion binding
D	0001522	biological_process	pseudouridine synthesis
D	0004730	molecular_function	pseudouridylate synthase activity
D	0005737	cellular_component	cytoplasm
D	0016798	molecular_function	hydrolase activity, acting on glycosyl bonds
D	0016829	molecular_function	lyase activity
D	0046113	biological_process	nucleobase catabolic process
D	0046872	molecular_function	metal ion binding
E	0001522	biological_process	pseudouridine synthesis
E	0004730	molecular_function	pseudouridylate synthase activity
E	0005737	cellular_component	cytoplasm
E	0016798	molecular_function	hydrolase activity, acting on glycosyl bonds
E	0016829	molecular_function	lyase activity
E	0046113	biological_process	nucleobase catabolic process
E	0046872	molecular_function	metal ion binding
F	0001522	biological_process	pseudouridine synthesis
F	0004730	molecular_function	pseudouridylate synthase activity
F	0005737	cellular_component	cytoplasm
F	0016798	molecular_function	hydrolase activity, acting on glycosyl bonds
F	0016829	molecular_function	lyase activity
F	0046113	biological_process	nucleobase catabolic process
F	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MN A 300

Chain	Residue
A	HIS-4
A	HIS-2
C	GLU204
C	GLU206
C	HOH612
E	HIS-5

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MN A 400

Chain	Residue
A	HOH606
A	HOH611
C	HOH604
A	ASP126
A	HOH602
A	HOH605

site_id	AC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MN B 300

Chain	Residue
A	GLU204
A	GLU206
A	HOH626
B	HIS-2
B	HIS-4
F	HIS-5

site_id	AC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MN B 400

Chain	Residue
A	HOH616
A	HOH636
B	ASP126
B	HOH604
B	HOH607
B	HOH609

site_id	AC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MN C 300

Chain	Residue
B	GLU204
B	GLU206
B	HOH614
C	HIS-2
C	HIS-4
D	HIS-5

site_id	AC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MN C 400

Chain	Residue
B	HOH613
C	ASP126
C	HOH610
C	HOH614
C	HOH621
C	HOH636

site_id	AC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MN D 300

Chain	Residue
C	HIS-5
D	HIS-2
D	HIS-4
E	GLU204
E	GLU206
E	HOH618

site_id	AC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MN D 400

Chain	Residue
D	ASP126
D	HOH603
D	HOH605
D	HOH609
E	HOH604
E	HOH606

site_id	AC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MN E 300

Chain	Residue
A	HIS-5
E	HIS-2
E	HIS-4
F	GLU204
F	GLU206
F	HOH605

site_id	BC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MN E 400

Chain	Residue
E	ASP126
E	HOH609
E	HOH611
E	HOH619
F	HOH618
F	HOH623

site_id	BC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MN F 300

Chain	Residue
B	HIS-5
D	GLU204
D	GLU206
D	HOH614
F	HIS-2
F	HIS-4

site_id	BC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MN F 400

Chain	Residue
D	HOH606
D	HOH607
F	ASP126
F	HOH601
F	HOH602
F	HOH603

site_id	BC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MN C 401

Chain	Residue
C	GLU64
C	GLU65
C	GLU68
C	HOH686
C	HOH716
C	HOH722

site_id	BC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MN A 401

Chain	Residue
A	GLU229
A	HOH808
A	HOH811
A	HOH818
F	GLU220

site_id	BC6
Number of Residues	7
Details	BINDING SITE FOR RESIDUE MN F 401

Chain	Residue
C	GLU4
F	GLU229
F	GLU233
F	HOH736
F	HOH745
F	HOH748
F	HOH755

site_id	BC7
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MN E 401

Chain	Residue
D	HOH760
E	HOH717

site_id	BC8
Number of Residues	19
Details	BINDING SITE FOR RESIDUE UNL A 600

Chain	Residue
A	SER128
A	ASP130
A	LYS147
A	HOH603
A	HOH606
A	HOH608
A	HOH610
A	HOH611
A	HOH612
A	HOH644
A	HOH662
A	HOH790
A	GLU17
A	THR19
A	LYS77
A	THR96
A	VAL97
A	THR114
A	GLY116

site_id	BC9
Number of Residues	19
Details	BINDING SITE FOR RESIDUE UNL B 600

Chain	Residue
A	HOH616
B	GLU17
B	THR19
B	LYS77
B	THR96
B	VAL97
B	THR114
B	GLY116
B	SER128
B	ASP130
B	LYS147
B	THR245
B	EDO601
B	HOH605
B	HOH609
B	HOH610
B	HOH625
B	HOH642
B	HOH644

site_id	CC1
Number of Residues	19
Details	BINDING SITE FOR RESIDUE UNL C 600

Chain	Residue
C	GLU17
C	THR19
C	LYS77
C	THR96
C	VAL97
C	THR114
C	GLY116
C	SER128
C	ASP130
C	LYS147
C	HOH605
C	HOH614
C	HOH629
C	HOH632
C	HOH636
C	HOH643
C	HOH646
C	HOH654
C	HOH736

site_id	CC2
Number of Residues	20
Details	BINDING SITE FOR RESIDUE UNL D 600

Chain	Residue
D	GLU17
D	THR19
D	LYS77
D	THR96
D	VAL97
D	THR114
D	GLY116
D	SER128
D	ASP130
D	LYS147
D	THR245
D	HOH608
D	HOH609
D	HOH612
D	HOH621
D	HOH633
D	HOH644
D	HOH659
D	HOH744
E	HOH604

site_id	CC3
Number of Residues	18
Details	BINDING SITE FOR RESIDUE UNL E 600

Chain	Residue
E	GLU17
E	THR19
E	LYS77
E	THR96
E	VAL97
E	THR114
E	GLY116
E	SER128
E	ASP130
E	LYS147
E	HOH608
E	HOH611
E	HOH616
E	HOH652
E	HOH678
E	HOH693
E	HOH700
F	HOH618

site_id	CC4
Number of Residues	18
Details	BINDING SITE FOR RESIDUE UNL F 600

Chain	Residue
D	HOH607
F	GLU17
F	THR19
F	LYS77
F	THR96
F	VAL97
F	THR114
F	GLY116
F	SER128
F	ASP130
F	LYS147
F	HOH602
F	HOH604
F	HOH608
F	HOH610
F	HOH626
F	HOH644
F	HOH659

site_id	CC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO D 601

Chain	Residue
D	ARG81
D	HOH624
D	HOH632
E	LEU166
E	PRO187

site_id	CC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO C 601

Chain	Residue
C	HIS-2
C	HIS-5
D	HIS-2
D	HIS-5

site_id	CC7
Number of Residues	10
Details	BINDING SITE FOR RESIDUE EDO B 601

Chain	Residue
B	GLU17
B	VAL20
B	THR114
B	GLY115
B	GLY116
B	LYS147
B	PHE177
B	ASN264
B	UNL600
B	HOH697

site_id	CC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO E 601

Chain	Residue
E	THR132
E	SER135
E	HOH708
E	HOH710
F	LEU162

site_id	CC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO B 602

Chain	Residue
B	PRO165
B	LEU166
B	HOH627
B	HOH664
C	ARG81

site_id	DC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 601

Chain	Residue
A	HIS-5
A	HIS-2
A	HIS-4
E	HIS-2

site_id	DC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO D 602

Chain	Residue
D	ASP76
D	VAL78
D	ILE85
D	VAL86
D	HOH657
E	ARG185

site_id	DC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO E 602

Chain	Residue
D	VAL127
E	MSE158
E	HOH610
E	HOH637

site_id	DC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO E 603

Chain	Residue
E	LEU150
E	ASP151
E	VAL152
E	GLU153
E	HOH654
E	HOH696
E	HOH702

site_id	DC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO C 602

Chain	Residue
C	ARG138
C	LYS203
C	HOH730
E	LYS-7

site_id	DC6
Number of Residues	8
Details	BINDING SITE FOR RESIDUE EDO B 603

Chain	Residue
B	HIS-2
B	HIS-5
B	HOH663
F	HIS-2
F	HIS-3
F	HIS-4
F	HIS-5
F	HOH704

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	6
Details	ACT_SITE: Proton donor => ECO:0000255\|HAMAP-Rule:MF_01876

Chain	Residue	Details
A	GLU17
B	GLU17
C	GLU17
D	GLU17
E	GLU17
F	GLU17

site_id	SWS_FT_FI2
Number of Residues	6
Details	ACT_SITE: Nucleophile => ECO:0000255\|HAMAP-Rule:MF_01876

Chain	Residue	Details
A	LYS147
B	LYS147
C	LYS147
D	LYS147
E	LYS147
F	LYS147

site_id	SWS_FT_FI3
Number of Residues	18
Details	BINDING: BINDING => ECO:0000255\|HAMAP-Rule:MF_01876

Chain	Residue	Details
C	LYS77
C	VAL97
C	SER128
D	LYS77
D	VAL97
D	SER128
E	LYS77
E	VAL97
E	SER128
F	LYS77
F	VAL97
F	SER128
A	LYS77
A	VAL97
A	SER128
B	LYS77
B	VAL97
B	SER128

site_id	SWS_FT_FI4
Number of Residues	6
Details	BINDING: BINDING => ECO:0000255\|HAMAP-Rule:MF_01876, ECO:0000269\|PubMed:15822122

Chain	Residue	Details
A	ASP126
B	ASP126
C	ASP126
D	ASP126
E	ASP126
F	ASP126

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