Summary Structural details Experimental details Functional details Sequence Neighbor Downloads

1FIQ

CRYSTAL STRUCTURE OF XANTHINE OXIDASE FROM BOVINE MILK

> Summary

Summary for 1FIQ

Related	1FO4
Descriptor	XANTHINE OXIDASE, FE2/S2 (INORGANIC) CLUSTER, FLAVIN-ADENINE DINUCLEOTIDE, ... (10 entities in total)
Functional Keywords	xanthine oxidase, oxidoreductase
Biological source	Bos taurus (cattle)
Cellular location	Cytoplasm P80457 P80457 P80457
Total number of polymer chains	3
Total molecular weight	148953.16
Authors	Enroth, C.,Eger, B.T.,Okamoto, K.,Nishino, T.,Nishino, T.,Pai, E.F. (deposition date: 2000-08-04, release date: 2000-10-04, Last modification date: 2017-02-01)
Primary citation	Enroth, C.,Eger, B.T.,Okamoto, K.,Nishino, T.,Nishino, T.,Pai, E.F. Crystal structures of bovine milk xanthine dehydrogenase and xanthine oxidase: structure-based mechanism of conversion. Proc.Natl.Acad.Sci.USA, 97:10723-10728, 2000 PubMed: 11005854 (PDB entries with the same primary citation) DOI: 10.1073/pnas.97.20.10723 Import into Mendeley
Experimental method	X-RAY DIFFRACTION (2.5 Å)

Structure validation

Download full validation report

More Asymmetric unit images

Molmil generated image of 1fiq — no rotation

More Biological unit images

(*)In the case of coarse surface representation, the asymmetric unit is shown as red ribbon representation.

Coordinate files for Biological unit (1fiq.pdb1.gz [409.38 KB])

> Structural details

Entity

Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
A	XANTHINE OXIDASE	polymer	219	24036.8	1	UniProt (P80457) Pfam (PF00111) Pfam (PF01799)	Bos taurus (cattle)@PDBj	XO
B	XANTHINE OXIDASE	polymer	350	39028.2	1	UniProt (P80457) Pfam (PF00941) Pfam (PF03450)	Bos taurus (cattle)@PDBj	XO
C	XANTHINE OXIDASE	polymer	763	83964.4	1	UniProt (P80457) Pfam (PF01315) Pfam (PF02738)	Bos taurus (cattle)@PDBj	XO
	FE2/S2 (INORGANIC) CLUSTER	non-polymer		175.8	2	FES
	FLAVIN-ADENINE DINUCLEOTIDE	non-polymer		785.6	1	FAD
	PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER	non-polymer		395.4	1	MTE
	DIOXOTHIOMOLYBDENUM(VI) ION	non-polymer		161.0	1	MOS
	2-HYDROXYBENZOIC ACID	non-polymer		138.1	1	SAL
	GLYCEROL	non-polymer		92.1	1	GOL
	water	water		18.0	596	HOH

Sequence viewer

Contents of the asymmetric unit

Polymers	Number of chains	3
Polymers	Total molecular weight	147029.4
Non-Polymers*	Number of molecules	7
Non-Polymers*	Total molecular weight	1923.8
All*	Total molecular weight	148953.2

*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:

X-RAY DIFFRACTION (2.5 Å)

Cell axes	117.831	165.403	154.447
Cell angles	90.00	90.00	90.00
Spacegroup	C 2 2 21
Resolution limits	8.00 - 2.50
the highest resolution shell value	2.590 - 2.500
R-factor	0.212
R-work	0.21200
the highest resolution shell value	0.287
R-free	0.27500
the highest resolution shell value	0.352
RMSD bond length	0.013
RMSD bond angle	1.400 (23.300*)

Data Collection Statistics

Resolution limits	30.00 - 2.50
the highest resolution shell value	-
Number of reflections	51300*
Completeness	97.9
the highest resolution shell value	97.5*
I/sigma(I)	-3

Crystallization Conditions

crystal ID	method	pH	pH range	temperature	unit
1	unknown*				K*

Crystallization Reagents

crystal ID

solution ID

reagent name

concentration

details

Crystallization Reagents in Literatures*

crystal ID

solution

reagent name

concentration (unit)

details

Annotated Information is extracted from Literature Info*

> Functional details

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0005829	cellular_component	cytosol
A	0005615	cellular_component	extracellular space
A	0005777	cellular_component	peroxisome
A	0002197	cellular_component	xanthine dehydrogenase complex
A	0051537	molecular_function	2 iron, 2 sulfur cluster binding
A	0009055	molecular_function	electron carrier activity
A	0071949	molecular_function	FAD binding
A	0050660	molecular_function	flavin adenine dinucleotide binding
A	0005506	molecular_function	iron ion binding
A	0030151	molecular_function	molybdenum ion binding
A	0043546	molecular_function	molybdopterin cofactor binding
A	0016614	molecular_function	oxidoreductase activity, acting on CH-OH group of donors
A	0016903	molecular_function	oxidoreductase activity, acting on the aldehyde or oxo group of donors
A	0042803	molecular_function	protein homodimerization activity
A	0004854	molecular_function	xanthine dehydrogenase activity
A	0004855	molecular_function	xanthine oxidase activity
A	0009115	biological_process	xanthine catabolic process
B	0005829	cellular_component	cytosol
B	0005615	cellular_component	extracellular space
B	0005777	cellular_component	peroxisome
B	0002197	cellular_component	xanthine dehydrogenase complex
B	0051537	molecular_function	2 iron, 2 sulfur cluster binding
B	0009055	molecular_function	electron carrier activity
B	0071949	molecular_function	FAD binding
B	0050660	molecular_function	flavin adenine dinucleotide binding
B	0005506	molecular_function	iron ion binding
B	0030151	molecular_function	molybdenum ion binding
B	0043546	molecular_function	molybdopterin cofactor binding
B	0016614	molecular_function	oxidoreductase activity, acting on CH-OH group of donors
B	0016903	molecular_function	oxidoreductase activity, acting on the aldehyde or oxo group of donors
B	0042803	molecular_function	protein homodimerization activity
B	0004854	molecular_function	xanthine dehydrogenase activity
B	0004855	molecular_function	xanthine oxidase activity
B	0009115	biological_process	xanthine catabolic process
C	0005829	cellular_component	cytosol
C	0005615	cellular_component	extracellular space
C	0005777	cellular_component	peroxisome
C	0002197	cellular_component	xanthine dehydrogenase complex
C	0051537	molecular_function	2 iron, 2 sulfur cluster binding
C	0009055	molecular_function	electron carrier activity
C	0071949	molecular_function	FAD binding
C	0050660	molecular_function	flavin adenine dinucleotide binding
C	0005506	molecular_function	iron ion binding
C	0030151	molecular_function	molybdenum ion binding
C	0043546	molecular_function	molybdopterin cofactor binding
C	0016614	molecular_function	oxidoreductase activity, acting on CH-OH group of donors
C	0016903	molecular_function	oxidoreductase activity, acting on the aldehyde or oxo group of donors
C	0042803	molecular_function	protein homodimerization activity
C	0004854	molecular_function	xanthine dehydrogenase activity
C	0004855	molecular_function	xanthine oxidase activity
C	0009115	biological_process	xanthine catabolic process

Functional Information from PDB Data

site_id

Number of Residues

Details

AC1

BINDING SITE FOR RESIDUE FES A 601

Chain	Residue
A	GLN112
A	CYS113
A	GLY114
A	CYS116
A	CYS148
A	ARG149
A	CYS150

AC2

BINDING SITE FOR RESIDUE FES A 602

Chain	Residue
A	GLY42
A	CYS43
A	GLY44
A	GLY46
A	GLY47
A	CYS48
A	GLY49
A	CYS51
A	ASN71
A	CYS73

AC3

BINDING SITE FOR RESIDUE MTE C 1333

Chain	Residue
A	GLN112
A	CYS150
C	GLY796
C	GLY797
C	PHE798
C	ARG912
C	MET1038
C	GLY1039
C	GLN1040
C	ALA1078
C	ALA1079
C	SER1080
C	VAL1081
C	SER1082
C	GLN1194
C	GLU1261
C	MOS1334
C	HOH1433
C	HOH1516
C	HOH1601

AC4

BINDING SITE FOR RESIDUE MOS C 1334

Chain	Residue
C	GLN767
C	PHE798
C	GLY799
C	PHE911
C	ARG912
C	ALA1078
C	ALA1079
C	GLU1261
C	MTE1333
C	SAL1335

AC5

BINDING SITE FOR RESIDUE SAL C 1335

Chain	Residue
C	GLU802
C	ARG880
C	PHE914
C	SER1008
C	PHE1009
C	THR1010
C	VAL1011
C	MOS1334
C	HOH1457

AC6

BINDING SITE FOR RESIDUE FAD B 606

Chain	Residue
A	GLU45
A	GLY46
B	LYS256
B	LEU257
B	VAL258
B	VAL259
B	GLY260
B	ASN261
B	THR262
B	GLU263
B	ILE264
B	LEU287
B	PHE337
B	ALA338
B	ALA346
B	SER347
B	GLY350
B	ASN351
B	ILE353
B	THR354
B	SER359
B	ASP360
B	LEU404
B	HOH714

AC7

BINDING SITE FOR RESIDUE GOL C 1336

Chain	Residue
C	ARG839
C	HIS840
C	ILE877
C	THR909
C	ALA910
C	PHE911
C	PHE914
C	GLY915
C	GLN918

Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_id

Number of Residues

Details

FES_1fiq_A_602

FE2/S2 (INORGANIC) CLUSTER binding site

Chain	Residue	ligand
A	LYS40-CYS51	FES: FE2/S2 (INORGANIC) CLUSTER
A	ASN71	FES: FE2/S2 (INORGANIC) CLUSTER
A	CYS73	FES: FE2/S2 (INORGANIC) CLUSTER

FAD_1fiq_B_606

FLAVIN-ADENINE DINUCLEOTIDE binding site

Chain	Residue	ligand
A	GLU45-GLY47	FAD: FLAVIN-ADENINE DINUCLEOTIDE
A	LEU74	FAD: FLAVIN-ADENINE DINUCLEOTIDE
B	LYS256-GLY265	FAD: FLAVIN-ADENINE DINUCLEOTIDE
B	GLU267	FAD: FLAVIN-ADENINE DINUCLEOTIDE
B	LEU287	FAD: FLAVIN-ADENINE DINUCLEOTIDE
B	ALA301	FAD: FLAVIN-ADENINE DINUCLEOTIDE
B	LEU305	FAD: FLAVIN-ADENINE DINUCLEOTIDE
B	TRP336-ALA338	FAD: FLAVIN-ADENINE DINUCLEOTIDE
B	VAL342	FAD: FLAVIN-ADENINE DINUCLEOTIDE
B	VAL345-SER347	FAD: FLAVIN-ADENINE DINUCLEOTIDE
B	GLY349-ASN351	FAD: FLAVIN-ADENINE DINUCLEOTIDE
B	ILE353-THR354	FAD: FLAVIN-ADENINE DINUCLEOTIDE
B	ILE358-LEU361	FAD: FLAVIN-ADENINE DINUCLEOTIDE
B	LEU398	FAD: FLAVIN-ADENINE DINUCLEOTIDE
B	GLU402-LEU404	FAD: FLAVIN-ADENINE DINUCLEOTIDE
B	LYS422	FAD: FLAVIN-ADENINE DINUCLEOTIDE
B	LYS433	FAD: FLAVIN-ADENINE DINUCLEOTIDE

FES_1fiq_A_601

FE2/S2 (INORGANIC) CLUSTER binding site

Chain	Residue	ligand
A	GLY110-THR117	FES: FE2/S2 (INORGANIC) CLUSTER
A	LEU147-THR151	FES: FE2/S2 (INORGANIC) CLUSTER
C	LEU744	FES: FE2/S2 (INORGANIC) CLUSTER

MTE_1fiq_C_1333

PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER binding site

Chain	Residue	ligand
A	GLN112-CYS113	MTE: PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER
A	CYS150	MTE: PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER
C	GLY796-GLY799	MTE: PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER
C	PHE911-ARG912	MTE: PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER
C	MET1038-GLN1040	MTE: PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER
C	LEU1042	MTE: PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER
C	THR1077-THR1083	MTE: PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER
C	GLN1194	MTE: PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER
C	GLY1260-GLU1261	MTE: PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER

MOS_1fiq_C_1334

DIOXOTHIOMOLYBDENUM(VI) ION binding site

Chain	Residue	ligand
C	GLN767	MOS: DIOXOTHIOMOLYBDENUM(VI) ION
C	PHE798-GLY799	MOS: DIOXOTHIOMOLYBDENUM(VI) ION
C	GLU802	MOS: DIOXOTHIOMOLYBDENUM(VI) ION
C	ALA910-PHE914	MOS: DIOXOTHIOMOLYBDENUM(VI) ION
C	THR1077-ALA1079	MOS: DIOXOTHIOMOLYBDENUM(VI) ION
C	GLU1261	MOS: DIOXOTHIOMOLYBDENUM(VI) ION

SAL_1fiq_C_1335

2-HYDROXYBENZOIC ACID binding site

Chain	Residue	ligand
C	GLU802	SAL: 2-HYDROXYBENZOIC ACID
C	LEU873	SAL: 2-HYDROXYBENZOIC ACID
C	SER876	SAL: 2-HYDROXYBENZOIC ACID
C	ARG880	SAL: 2-HYDROXYBENZOIC ACID
C	PHE914	SAL: 2-HYDROXYBENZOIC ACID
C	SER1008-VAL1011	SAL: 2-HYDROXYBENZOIC ACID
C	LEU1014	SAL: 2-HYDROXYBENZOIC ACID
C	ALA1078-ALA1079	SAL: 2-HYDROXYBENZOIC ACID

GOL_1fiq_C_1336

GLYCEROL binding site

Chain	Residue	ligand
C	GLY838-HIS840	GOL: GLYCEROL
C	ILE877	GOL: GLYCEROL
C	THR909-PHE911	GOL: GLYCEROL
C	GLY913-GLN918	GOL: GLYCEROL

Functional Information from PROSITE/UniProt

site_id

Number of Residues

Details

PS00559

Eukaryotic molybdopterin oxidoreductases signature. [GA]-{A}-x(2)-[KRNQHT]-x(11,14)-[LIVMFYWS]-x(3)-{V}-{GK}-x(3)-[LIVMF]-x

Chain	Residue	Details
C	GLY797-ASP832

Functional Information from SwissProt/UniProt

site_id

Number of Residues

Details

SWS_FT_FI1

Proton acceptor. {ECO:0000269|PubMed:15148401}.

Chain	Residue	Details
A	NA*

SWS_FT_FI2

Iron-sulfur 2

Chain	Residue	Details
A	CYS113
A	CYS116
A	CYS148
A	CYS150

SWS_FT_FI3

Molybdenum; via carbonyl oxygen

Chain	Residue	Details
A	NA*

SWS_FT_FI4

Iron-sulfur 1

Chain	Residue	Details
A	CYS43
A	CYS48
A	CYS51
A	CYS73

SWS_FT_FI5

Molybdenum; via amide nitrogen

Chain	Residue	Details
A	NA*
A	NA*

SWS_FT_FI6

Molybdenum

Chain	Residue	Details
A	NA*

SWS_FT_FI7

Substrate.

Chain	Residue	Details
A	NA*
A	NA*
A	NA*

SWS_FT_FI8

FAD; via amide nitrogen and carbonyl oxygen. {ECO:0000269|PubMed:12421831, ECO:0000269|PubMed:15148401}.

Chain	Residue	Details
A	NA*

SWS_FT_FI9

Substrate; via amide nitrogen.

Chain	Residue	Details
A	NA*

SWS_FT_FI10

FAD. {ECO:0000269|PubMed:12421831, ECO:0000269|PubMed:15148401}.

Chain	Residue	Details
A	NA*
A	NA*
A	NA*

SWS_FT_FI11

FAD. {ECO:0000269|PubMed:12421831, ECO:0000269|PubMed:15148401}.

Chain	Residue	Details
A	NA*
A	NA*

SWS_FT_FI12

Proton acceptor. {ECO:0000269|PubMed:15148401}.

Chain	Residue	Details
B	NA*

SWS_FT_FI13

Iron-sulfur 2

Chain	Residue	Details
B	NA*
B	NA*
B	NA*
B	NA*

SWS_FT_FI14

Molybdenum; via carbonyl oxygen

Chain	Residue	Details
B	NA*

SWS_FT_FI15

Iron-sulfur 1

Chain	Residue	Details
B	NA*
B	NA*
B	NA*
B	NA*

SWS_FT_FI16

Molybdenum; via amide nitrogen

Chain	Residue	Details
B	NA*
B	NA*

SWS_FT_FI17

Molybdenum

Chain	Residue	Details
B	NA*

SWS_FT_FI18

Substrate.

Chain	Residue	Details
B	NA*
B	NA*
B	NA*

SWS_FT_FI19

FAD; via amide nitrogen and carbonyl oxygen. {ECO:0000269|PubMed:12421831, ECO:0000269|PubMed:15148401}.

Chain	Residue	Details
B	LEU185

SWS_FT_FI20

Substrate; via amide nitrogen.

Chain	Residue	Details
B	NA*

SWS_FT_FI21

FAD. {ECO:0000269|PubMed:12421831, ECO:0000269|PubMed:15148401}.

Chain	Residue	Details
B	PHE118
B	ASP141
B	LYS203

SWS_FT_FI22

FAD. {ECO:0000269|PubMed:12421831, ECO:0000269|PubMed:15148401}.

Chain	Residue	Details
B	LEU38-ILE45
B	SER128-ASN132

SWS_FT_FI23

Proton acceptor. {ECO:0000269|PubMed:15148401}.

Chain	Residue	Details
C	GLU692

SWS_FT_FI24

Iron-sulfur 2

Chain	Residue	Details
C	NA*
C	NA*
C	NA*
C	NA*

SWS_FT_FI25

Molybdenum; via carbonyl oxygen

Chain	Residue	Details
C	PHE229

SWS_FT_FI26

Iron-sulfur 1

Chain	Residue	Details
C	NA*
C	NA*
C	NA*
C	NA*

SWS_FT_FI27

Molybdenum; via amide nitrogen

Chain	Residue	Details
C	ARG343
C	ALA510

SWS_FT_FI28

Molybdenum

Chain	Residue	Details
C	GLN198

SWS_FT_FI29

Substrate.

Chain	Residue	Details
C	GLU233
C	ARG311
C	PHE345

SWS_FT_FI30

FAD; via amide nitrogen and carbonyl oxygen. {ECO:0000269|PubMed:12421831, ECO:0000269|PubMed:15148401}.

Chain	Residue	Details
C	NA*

SWS_FT_FI31

Substrate; via amide nitrogen.

Chain	Residue	Details
C	THR441

SWS_FT_FI32

FAD. {ECO:0000269|PubMed:12421831, ECO:0000269|PubMed:15148401}.

Chain	Residue	Details
C	NA*
C	NA*
C	NA*

SWS_FT_FI33

FAD. {ECO:0000269|PubMed:12421831, ECO:0000269|PubMed:15148401}.

Chain	Residue	Details
C	NA*
C	NA*

CSA1

a catalytic site defined by CSA, PubMed 19109252, 15148401

Chain	Residue	Details
C	GLU1261
C	ARG880
C	GLU802

Catalytic Information from CSA

site_id

Number of Residues

Details

CSA1

a catalytic site defined by CSA, PubMed 19109252, 15148401

Chain	Residue	Details
C	GLU1261
C	ARG880
C	GLU802

> Sequence Neighbor

Sequence navigator - 1fiq: Chain A

Sequence navigator - 1fiq: Chain B

Sequence navigator - 1fiq: Chain C

> Downloads

Resources

File format		File name (file size)
PDB	all	pdb1fiq.ent.gz (215.25 KB) Display
	all (no-compress)	pdb1fiq.ent (880 KB)
	header only	pdb1fiq.ent.gz (11.7 KB) Display
PDBx/mmCIF	1fiq.cif.gz (267.68 KB) Display Flat file Tree view Header
PDBML	all	1fiq.xml.gz (357.89 KB) Display
	no-atom	1fiq-noatom.xml.gz (53.95 KB) Display
	ext-atom	1fiq-extatom.xml.gz (229.71 KB) Display
PDBMLplus	all	1fiq-plus.xml.gz (364.11 KB) Display
	no-atom	1fiq-plus-noatom.xml.gz (60.17 KB) Display
	add only	1fiq-add.xml.gz (6.22 KB) Display
RDF		1fiq.rdf.gz (129.01 KB) Display
Biological unit (PDB format)		1fiq.pdb1.gz (409.38 KB) (A,B,C) *author and software defined assembly, 6 molecule(s) (hexameric) Display
Validation reports	PDF	1fiq_validation.pdf.gz (460.34 KB) Display
	PDF-full	1fiq_full_validation.pdf.gz (500.84 KB) Display
	XML	1fiq_validation.xml.gz (29.89 KB) Display
	PNG	1fiq_multipercentile_validation.png.gz (109.61 KB) Display
	SVG	1fiq_multipercentile_validation.svg.gz (810 B) Display
Sequence (fasta)	1fiq_seq.txt Display

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134436

entries
(2017-10-18)

134436

entries available on 2017-10-18
00:00 UTC / 09:00 JST

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)