Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4H2H

Crystal structure of an enolase (mandalate racemase subgroup, target EFI-502101) from Pelagibaca bermudensis htcc2601, with bound mg and l-4-hydroxyproline betaine (betonicine)

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000287	molecular_function	magnesium ion binding
A	0006579	biological_process	amino-acid betaine catabolic process
A	0016853	molecular_function	isomerase activity
A	0016855	molecular_function	racemase and epimerase activity, acting on amino acids and derivatives
A	0046872	molecular_function	metal ion binding
A	0047661	molecular_function	amino-acid racemase activity
B	0000287	molecular_function	magnesium ion binding
B	0006579	biological_process	amino-acid betaine catabolic process
B	0016853	molecular_function	isomerase activity
B	0016855	molecular_function	racemase and epimerase activity, acting on amino acids and derivatives
B	0046872	molecular_function	metal ion binding
B	0047661	molecular_function	amino-acid racemase activity
C	0000287	molecular_function	magnesium ion binding
C	0006579	biological_process	amino-acid betaine catabolic process
C	0016853	molecular_function	isomerase activity
C	0016855	molecular_function	racemase and epimerase activity, acting on amino acids and derivatives
C	0046872	molecular_function	metal ion binding
C	0047661	molecular_function	amino-acid racemase activity
D	0000287	molecular_function	magnesium ion binding
D	0006579	biological_process	amino-acid betaine catabolic process
D	0016853	molecular_function	isomerase activity
D	0016855	molecular_function	racemase and epimerase activity, acting on amino acids and derivatives
D	0046872	molecular_function	metal ion binding
D	0047661	molecular_function	amino-acid racemase activity
E	0000287	molecular_function	magnesium ion binding
E	0006579	biological_process	amino-acid betaine catabolic process
E	0016853	molecular_function	isomerase activity
E	0016855	molecular_function	racemase and epimerase activity, acting on amino acids and derivatives
E	0046872	molecular_function	metal ion binding
E	0047661	molecular_function	amino-acid racemase activity
F	0000287	molecular_function	magnesium ion binding
F	0006579	biological_process	amino-acid betaine catabolic process
F	0016853	molecular_function	isomerase activity
F	0016855	molecular_function	racemase and epimerase activity, acting on amino acids and derivatives
F	0046872	molecular_function	metal ion binding
F	0047661	molecular_function	amino-acid racemase activity
G	0000287	molecular_function	magnesium ion binding
G	0006579	biological_process	amino-acid betaine catabolic process
G	0016853	molecular_function	isomerase activity
G	0016855	molecular_function	racemase and epimerase activity, acting on amino acids and derivatives
G	0046872	molecular_function	metal ion binding
G	0047661	molecular_function	amino-acid racemase activity
H	0000287	molecular_function	magnesium ion binding
H	0006579	biological_process	amino-acid betaine catabolic process
H	0016853	molecular_function	isomerase activity
H	0016855	molecular_function	racemase and epimerase activity, acting on amino acids and derivatives
H	0046872	molecular_function	metal ion binding
H	0047661	molecular_function	amino-acid racemase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG A 401

Chain	Residue
A	GLN161
A	ASP193
A	GLU218
A	ASP241
A	0XW403
A	HOH550

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE NI A 402

Chain	Residue
C	HOH507
E	HIS235
H	HIS235
A	HIS235
C	HIS235
C	HOH505

site_id	AC3
Number of Residues	13
Details	BINDING SITE FOR RESIDUE 0XW A 403

Chain	Residue
A	TYR20
A	TYR56
A	TYR134
A	GLN161
A	LYS163
A	ASP193
A	ASN195
A	GLU218
A	ASP241
A	LYS265
A	ALA294
A	TRP320
A	MG401

site_id	AC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE IOD A 404

Chain	Residue
A	GLY185
A	GLY187
C	HOH549

site_id	AC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE IOD A 405

Chain	Residue
A	SER246
A	LEU247
A	ASN248

site_id	AC6
Number of Residues	1
Details	BINDING SITE FOR RESIDUE IOD A 406

Chain	Residue
A	ARG314

site_id	AC7
Number of Residues	1
Details	BINDING SITE FOR RESIDUE IOD A 407

Chain	Residue
A	HOH663

site_id	AC8
Number of Residues	1
Details	BINDING SITE FOR RESIDUE IOD A 409

Chain	Residue
A	LYS36

site_id	AC9
Number of Residues	1
Details	BINDING SITE FOR RESIDUE IOD A 410

Chain	Residue
A	HIS329

site_id	BC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG B 401

Chain	Residue
B	GLN161
B	ASP193
B	GLU218
B	ASP241
B	0XW403
B	HOH551

site_id	BC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE NI B 402

Chain	Residue
B	HIS235
D	HIS235
D	HOH528
F	HIS235
F	HOH510
G	HIS235

site_id	BC3
Number of Residues	14
Details	BINDING SITE FOR RESIDUE 0XW B 403

Chain	Residue
B	TYR20
B	TYR56
B	TYR134
B	SER136
B	GLN161
B	LYS163
B	ASP193
B	ASN195
B	GLU218
B	ASP241
B	LYS265
B	ALA294
B	TRP320
B	MG401

site_id	BC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE IOD B 404

Chain	Residue
B	GLY185
B	GLY187
F	HOH566

site_id	BC5
Number of Residues	1
Details	BINDING SITE FOR RESIDUE IOD B 405

Chain	Residue
B	ARG314

site_id	BC6
Number of Residues	1
Details	BINDING SITE FOR RESIDUE IOD B 407

Chain	Residue
B	ARG88

site_id	BC7
Number of Residues	1
Details	BINDING SITE FOR RESIDUE IOD B 408

Chain	Residue
B	HOH787

site_id	BC8
Number of Residues	1
Details	BINDING SITE FOR RESIDUE IOD B 409

Chain	Residue
B	HIS329

site_id	BC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG C 401

Chain	Residue
C	GLN161
C	ASP193
C	GLU218
C	ASP241
C	0XW402
C	HOH514

site_id	CC1
Number of Residues	14
Details	BINDING SITE FOR RESIDUE 0XW C 402

Chain	Residue
C	TYR20
C	VAL52
C	TYR56
C	TYR134
C	GLN161
C	LYS163
C	ASP193
C	ASN195
C	GLU218
C	ASP241
C	LYS265
C	ALA294
C	TRP320
C	MG401

site_id	CC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE MPD C 403

Chain	Residue
C	LYS178
C	GLU181
F	ALA146
F	LYS178
F	GLU181
F	ALA182
F	HOH663

site_id	CC3
Number of Residues	2
Details	BINDING SITE FOR RESIDUE IOD C 404

Chain	Residue
C	GLU141
C	ARG167

site_id	CC4
Number of Residues	1
Details	BINDING SITE FOR RESIDUE IOD C 405

Chain	Residue
C	HOH709

site_id	CC5
Number of Residues	1
Details	BINDING SITE FOR RESIDUE IOD C 406

Chain	Residue
C	ARG314

site_id	CC6
Number of Residues	1
Details	BINDING SITE FOR RESIDUE IOD C 407

Chain	Residue
C	ARG147

site_id	CC7
Number of Residues	3
Details	BINDING SITE FOR RESIDUE IOD C 410

Chain	Residue
C	GLY185
C	GLY187
H	HOH591

site_id	CC8
Number of Residues	1
Details	BINDING SITE FOR RESIDUE IOD C 412

Chain	Residue
C	GLU141

site_id	CC9
Number of Residues	1
Details	BINDING SITE FOR RESIDUE IOD C 413

Chain	Residue
C	HIS329

site_id	DC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG D 401

Chain	Residue
D	GLN161
D	ASP193
D	GLU218
D	ASP241
D	0XW402
D	HOH524

site_id	DC2
Number of Residues	15
Details	BINDING SITE FOR RESIDUE 0XW D 402

Chain	Residue
D	TYR20
D	VAL52
D	TYR56
D	TYR134
D	SER136
D	GLN161
D	LYS163
D	ASP193
D	ASN195
D	GLU218
D	ASP241
D	LYS265
D	ALA294
D	TRP320
D	MG401

site_id	DC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MPD D 403

Chain	Residue
C	PHE224
C	GLU228
D	PHE224
D	HOH623
D	HOH631

site_id	DC4
Number of Residues	1
Details	BINDING SITE FOR RESIDUE IOD D 404

Chain	Residue
D	ARG167

site_id	DC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE IOD D 405

Chain	Residue
B	HOH609
D	GLY185
D	GLY187

site_id	DC6
Number of Residues	1
Details	BINDING SITE FOR RESIDUE IOD D 406

Chain	Residue
D	HOH638

site_id	DC7
Number of Residues	1
Details	BINDING SITE FOR RESIDUE IOD D 407

Chain	Residue
D	ARG314

site_id	DC8
Number of Residues	1
Details	BINDING SITE FOR RESIDUE IOD D 408

Chain	Residue
D	ARG88

site_id	DC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE IOD D 409

Chain	Residue
D	PRO19
D	TYR20
D	ARG21
D	GLY138
D	HOH713

site_id	EC1
Number of Residues	1
Details	BINDING SITE FOR RESIDUE IOD D 410

Chain	Residue
D	ASN17

site_id	EC2
Number of Residues	2
Details	BINDING SITE FOR RESIDUE IOD D 411

Chain	Residue
D	ILE44
D	LYS113

site_id	EC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG E 401

Chain	Residue
E	GLN161
E	ASP193
E	GLU218
E	ASP241
E	0XW402
E	HOH738

site_id	EC4
Number of Residues	12
Details	BINDING SITE FOR RESIDUE 0XW E 402

Chain	Residue
E	VAL52
E	TYR56
E	TYR134
E	SER136
E	GLN161
E	LYS163
E	ASP193
E	GLU218
E	ASP241
E	LYS265
E	ALA294
E	MG401

site_id	EC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MPD E 403

Chain	Residue
E	PHE224
E	GLU228
E	HOH616
E	HOH649
F	PHE224
F	GLU228

site_id	EC6
Number of Residues	1
Details	BINDING SITE FOR RESIDUE IOD E 404

Chain	Residue
E	ARG167

site_id	EC7
Number of Residues	1
Details	BINDING SITE FOR RESIDUE IOD E 405

Chain	Residue
E	ARG314

site_id	EC8
Number of Residues	1
Details	BINDING SITE FOR RESIDUE IOD E 406

Chain	Residue
E	HOH693

site_id	EC9
Number of Residues	1
Details	BINDING SITE FOR RESIDUE IOD E 407

Chain	Residue
E	ARG88

site_id	FC1
Number of Residues	1
Details	BINDING SITE FOR RESIDUE IOD E 408

Chain	Residue
E	VAL139

site_id	FC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE IOD E 409

Chain	Residue
E	ILE44
E	LYS113
E	HOH710
E	HOH735

site_id	FC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE IOD E 410

Chain	Residue
A	HOH602
E	GLY185
E	GLY187

site_id	FC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG F 401

Chain	Residue
F	GLN161
F	ASP193
F	GLU218
F	ASP241
F	0XW402
F	HOH571

site_id	FC5
Number of Residues	14
Details	BINDING SITE FOR RESIDUE 0XW F 402

Chain	Residue
F	TYR20
F	VAL52
F	TYR56
F	TYR134
F	GLN161
F	LYS163
F	ASP193
F	ASN195
F	GLU218
F	ASP241
F	LYS265
F	ALA294
F	TRP320
F	MG401

site_id	FC6
Number of Residues	1
Details	BINDING SITE FOR RESIDUE IOD F 403

Chain	Residue
F	HOH667

site_id	FC7
Number of Residues	1
Details	BINDING SITE FOR RESIDUE IOD F 404

Chain	Residue
F	ARG167

site_id	FC8
Number of Residues	2
Details	BINDING SITE FOR RESIDUE IOD F 406

Chain	Residue
F	GLY185
F	GLY187

site_id	FC9
Number of Residues	1
Details	BINDING SITE FOR RESIDUE IOD F 407

Chain	Residue
F	ARG314

site_id	GC1
Number of Residues	2
Details	BINDING SITE FOR RESIDUE IOD F 410

Chain	Residue
F	MET140
F	GLU141

site_id	GC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG G 401

Chain	Residue
G	GLN161
G	ASP193
G	GLU218
G	ASP241
G	0XW402
G	HOH517

site_id	GC3
Number of Residues	13
Details	BINDING SITE FOR RESIDUE 0XW G 402

Chain	Residue
G	VAL52
G	TYR56
G	TYR134
G	GLN161
G	LYS163
G	ASP193
G	ASN195
G	GLU218
G	ASP241
G	LYS265
G	ALA294
G	TRP320
G	MG401

site_id	GC4
Number of Residues	1
Details	BINDING SITE FOR RESIDUE IOD G 403

Chain	Residue
G	ARG314

site_id	GC5
Number of Residues	1
Details	BINDING SITE FOR RESIDUE IOD G 404

Chain	Residue
G	HOH614

site_id	GC6
Number of Residues	1
Details	BINDING SITE FOR RESIDUE IOD G 405

Chain	Residue
G	ARG167

site_id	GC7
Number of Residues	1
Details	BINDING SITE FOR RESIDUE IOD G 406

Chain	Residue
G	HIS329

site_id	GC8
Number of Residues	2
Details	BINDING SITE FOR RESIDUE IOD G 407

Chain	Residue
G	ILE44
G	LYS113

site_id	GC9
Number of Residues	1
Details	BINDING SITE FOR RESIDUE IOD G 408

Chain	Residue
G	ARG88

site_id	HC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE IOD G 409

Chain	Residue
D	HOH641
G	GLY185
G	GLY187

site_id	HC2
Number of Residues	1
Details	BINDING SITE FOR RESIDUE IOD G 410

Chain	Residue
G	GLU141

site_id	HC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG H 401

Chain	Residue
H	GLN161
H	ASP193
H	GLU218
H	ASP241
H	0XW402
H	HOH515

site_id	HC4
Number of Residues	13
Details	BINDING SITE FOR RESIDUE 0XW H 402

Chain	Residue
H	TYR20
H	VAL52
H	TYR56
H	GLN161
H	LYS163
H	ASP193
H	ASN195
H	GLU218
H	ASP241
H	LYS265
H	ALA294
H	TRP320
H	MG401

site_id	HC5
Number of Residues	1
Details	BINDING SITE FOR RESIDUE IOD H 403

Chain	Residue
H	ARG314

site_id	HC6
Number of Residues	1
Details	BINDING SITE FOR RESIDUE IOD H 404

Chain	Residue
H	HOH645

site_id	HC7
Number of Residues	1
Details	BINDING SITE FOR RESIDUE IOD H 405

Chain	Residue
H	ARG167

site_id	HC8
Number of Residues	2
Details	BINDING SITE FOR RESIDUE IOD H 406

Chain	Residue
H	MET140
H	GLU141

site_id	HC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE IOD H 408

Chain	Residue
E	HOH591
H	GLY185
H	GLY187

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	16
Details	Active site: {"description":"Proton donor/acceptor","evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	48
Details	Binding site: {}

Chain

Residue

Details

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	6
Details	M-CSA 940

Chain	Residue	Details
A	LYS163	proton shuttle (general acid/base)
A	ASP193	metal ligand
A	GLU218	metal ligand
A	ASP241	metal ligand
A	LYS265	proton shuttle (general acid/base)
A	TRP320	electrostatic stabiliser

site_id	MCSA2
Number of Residues	6
Details	M-CSA 940

Chain	Residue	Details
B	LYS163	proton shuttle (general acid/base)
B	ASP193	metal ligand
B	GLU218	metal ligand
B	ASP241	metal ligand
B	LYS265	proton shuttle (general acid/base)
B	TRP320	electrostatic stabiliser

site_id	MCSA3
Number of Residues	6
Details	M-CSA 940

Chain	Residue	Details
C	LYS163	proton shuttle (general acid/base)
C	ASP193	metal ligand
C	GLU218	metal ligand
C	ASP241	metal ligand
C	LYS265	proton shuttle (general acid/base)
C	TRP320	electrostatic stabiliser

site_id	MCSA4
Number of Residues	6
Details	M-CSA 940

Chain	Residue	Details
D	LYS163	proton shuttle (general acid/base)
D	ASP193	metal ligand
D	GLU218	metal ligand
D	ASP241	metal ligand
D	LYS265	proton shuttle (general acid/base)
D	TRP320	electrostatic stabiliser

site_id	MCSA5
Number of Residues	6
Details	M-CSA 940

Chain	Residue	Details
E	LYS163	proton shuttle (general acid/base)
E	ASP193	metal ligand
E	GLU218	metal ligand
E	ASP241	metal ligand
E	LYS265	proton shuttle (general acid/base)
E	TRP320	electrostatic stabiliser

site_id	MCSA6
Number of Residues	6
Details	M-CSA 940

Chain	Residue	Details
F	LYS163	proton shuttle (general acid/base)
F	ASP193	metal ligand
F	GLU218	metal ligand
F	ASP241	metal ligand
F	LYS265	proton shuttle (general acid/base)
F	TRP320	electrostatic stabiliser

site_id	MCSA7
Number of Residues	6
Details	M-CSA 940

Chain	Residue	Details
G	LYS163	proton shuttle (general acid/base)
G	ASP193	metal ligand
G	GLU218	metal ligand
G	ASP241	metal ligand
G	LYS265	proton shuttle (general acid/base)
G	TRP320	electrostatic stabiliser

site_id	MCSA8
Number of Residues	6
Details	M-CSA 940

Chain	Residue	Details
H	LYS163	proton shuttle (general acid/base)
H	ASP193	metal ligand
H	GLU218	metal ligand
H	ASP241	metal ligand
H	LYS265	proton shuttle (general acid/base)
H	TRP320	electrostatic stabiliser

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