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1JRX
Asym. Unit
Info
Asym.Unit (223 KB)
Biol.Unit 1 (109 KB)
Biol.Unit 2 (111 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF ARG402ALA MUTANT FLAVOCYTOCHROME C3 FROM SHEWANELLA FRIGIDIMARINA
Authors
:
C. G. Mowat, R. Moysey, C. S. Miles, D. Leys, M. K. Doherty, P. Taylor, M. D. Walkinshaw, G. A. Reid, S. K. Chapman
Date
:
15 Aug 01 (Deposition) - 02 Nov 01 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Fumarate Reductase, Mutant, Flavocytochrome, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. G. Mowat, R. Moysey, C. S. Miles, D. Leys, M. K. Doherty, P. Taylor, M. D. Walkinshaw, G. A. Reid, S. K. Chapman
Kinetic And Crystallographic Analysis Of The Key Active Site Acid/Base Arginine In A Soluble Fumarate Reductase.
Biochemistry V. 40 12292 2001
(for further references see the
PDB file header
)
[
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Hetero Components
(4, 14)
Info
All Hetero Components
1a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
1b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
2a: FUMARIC ACID (FUMa)
2b: FUMARIC ACID (FUMb)
3a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
3b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
3c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
3d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
3e: PROTOPORPHYRIN IX CONTAINING FE (HEMe)
3f: PROTOPORPHYRIN IX CONTAINING FE (HEMf)
3g: PROTOPORPHYRIN IX CONTAINING FE (HEMg)
3h: PROTOPORPHYRIN IX CONTAINING FE (HEMh)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FAD
2
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
2
FUM
2
Ligand/Ion
FUMARIC ACID
3
HEM
8
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
4
NA
2
Ligand/Ion
SODIUM ION
[
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]
Sites
(14, 14)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR A:506 , MET A:507 , GLY A:508 , GLU A:534 , THR A:536 , HOH A:1811
BINDING SITE FOR RESIDUE NA A 1810
02
AC2
SOFTWARE
THR B:506 , MET B:507 , GLY B:508 , GLU B:534 , THR B:536 , HOH B:3033
BINDING SITE FOR RESIDUE NA B 2810
03
AC3
SOFTWARE
HIS A:8 , VAL A:9 , CYS A:14 , CYS A:17 , HIS A:18 , LEU A:24 , THR A:69 , SER A:73 , ALA A:74 , HIS A:75 , TYR A:298 , HEM A:802 , HOH A:2056 , HOH A:2151 , HOH A:2172 , HOH A:2221
BINDING SITE FOR RESIDUE HEM A 801
04
AC4
SOFTWARE
LEU A:4 , PHE A:7 , HIS A:8 , GLN A:12 , SER A:16 , CYS A:17 , CYS A:36 , CYS A:39 , HIS A:40 , HIS A:72 , TYR A:94 , HEM A:801 , HEM A:803 , HOH A:1877 , HOH A:1909 , HOH A:2075 , HOH A:2226 , HOH A:2540
BINDING SITE FOR RESIDUE HEM A 802
05
AC5
SOFTWARE
HIS A:40 , GLY A:41 , LEU A:43 , VAL A:46 , THR A:49 , THR A:50 , HIS A:52 , ALA A:57 , HIS A:58 , VAL A:66 , ALA A:67 , CYS A:68 , CYS A:71 , HIS A:72 , VAL A:80 , CYS A:82 , PHE A:90 , ASN A:91 , MET A:92 , HEM A:802 , HEM A:804 , HOH A:1815 , HOH A:2164 , HOH A:2321
BINDING SITE FOR RESIDUE HEM A 803
06
AC6
SOFTWARE
HIS A:54 , TYR A:55 , ASN A:56 , SER A:60 , HIS A:61 , PHE A:62 , CYS A:82 , SER A:84 , CYS A:85 , HIS A:86 , PHE A:88 , LEU A:167 , GLN A:338 , VAL A:374 , LYS A:431 , LYS A:434 , TYR A:435 , HEM A:803 , HOH A:1887 , HOH A:1973 , HOH A:1976 , HOH A:2080 , HOH A:2091 , HOH A:2123 , HOH A:2225 , HOH A:2245 , HOH A:2312
BINDING SITE FOR RESIDUE HEM A 804
07
AC7
SOFTWARE
HIS B:8 , VAL B:9 , CYS B:14 , CYS B:17 , HIS B:18 , LEU B:24 , SER B:73 , ALA B:74 , HIS B:75 , TYR B:298 , HEM B:802 , HOH B:1278 , HOH B:1394 , HOH B:1552 , HOH B:1638 , HOH B:1771 , HOH B:3041 , HOH B:3284
BINDING SITE FOR RESIDUE HEM B 801
08
AC8
SOFTWARE
LEU B:4 , PHE B:7 , HIS B:8 , GLN B:12 , SER B:16 , CYS B:17 , GLN B:35 , CYS B:36 , CYS B:39 , HIS B:40 , HIS B:72 , PRO B:93 , TYR B:94 , HEM B:801 , HEM B:803 , HOH B:1469 , HOH B:1556 , HOH B:2128 , HOH B:2192 , HOH B:3090 , HOH B:3181
BINDING SITE FOR RESIDUE HEM B 802
09
AC9
SOFTWARE
HIS B:40 , LEU B:43 , VAL B:46 , HIS B:52 , ALA B:57 , HIS B:58 , VAL B:66 , ALA B:67 , CYS B:68 , CYS B:71 , HIS B:72 , PHE B:90 , ASN B:91 , MET B:92 , HEM B:802 , HEM B:804 , HOH B:1021 , HOH B:1202 , HOH B:1942
BINDING SITE FOR RESIDUE HEM B 803
10
BC1
SOFTWARE
HIS B:54 , ASN B:56 , SER B:60 , HIS B:61 , PHE B:62 , CYS B:82 , SER B:84 , CYS B:85 , HIS B:86 , PHE B:88 , LEU B:167 , GLN B:338 , VAL B:374 , LYS B:431 , LYS B:434 , TYR B:435 , HEM B:803 , HOH B:1006 , HOH B:1454 , HOH B:1568 , HOH B:1594 , HOH B:1681 , HOH B:1731 , HOH B:1884
BINDING SITE FOR RESIDUE HEM B 804
11
BC2
SOFTWARE
VAL A:132 , GLY A:133 , SER A:134 , GLY A:135 , GLY A:136 , ALA A:137 , GLU A:156 , LYS A:157 , GLU A:158 , GLY A:162 , GLY A:163 , ASN A:164 , ALA A:165 , LEU A:167 , ALA A:168 , ALA A:169 , GLY A:170 , GLY A:171 , THR A:276 , ARG A:277 , GLY A:278 , ALA A:312 , THR A:313 , GLY A:314 , THR A:336 , ASN A:337 , GLN A:338 , ASP A:344 , MET A:375 , HIS A:504 , HIS A:505 , GLY A:533 , GLU A:534 , ARG A:544 , GLY A:547 , ASN A:548 , ALA A:549 , ILE A:550 , ILE A:553 , FUM A:1806 , HOH A:1819 , HOH A:1869 , HOH A:1889 , HOH A:1905 , HOH A:1911
BINDING SITE FOR RESIDUE FAD A 1805
12
BC3
SOFTWARE
VAL B:132 , GLY B:133 , GLY B:135 , GLY B:136 , ALA B:137 , GLU B:156 , LYS B:157 , GLU B:158 , GLY B:162 , GLY B:163 , ASN B:164 , ALA B:165 , LEU B:167 , ALA B:168 , ALA B:169 , GLY B:170 , GLY B:171 , THR B:276 , ARG B:277 , GLY B:278 , ALA B:312 , THR B:313 , GLY B:314 , THR B:336 , ASN B:337 , GLN B:338 , ASP B:344 , MET B:375 , HIS B:504 , HIS B:505 , GLY B:533 , GLU B:534 , ARG B:544 , GLY B:547 , ASN B:548 , ALA B:549 , ILE B:550 , ILE B:553 , HOH B:1009 , HOH B:1042 , HOH B:1057 , HOH B:1150 , HOH B:1208 , FUM B:2806 , HOH B:3035
BINDING SITE FOR RESIDUE FAD B 2805
13
BC4
SOFTWARE
GLY A:170 , MET A:236 , HIS A:365 , MET A:375 , THR A:377 , GLU A:378 , HIS A:504 , ARG A:544 , GLY A:546 , GLY A:547 , FAD A:1805
BINDING SITE FOR RESIDUE FUM A 1806
14
BC5
SOFTWARE
GLY B:170 , MET B:236 , HIS B:365 , MET B:375 , THR B:377 , GLU B:378 , HIS B:504 , ARG B:544 , GLY B:546 , GLY B:547 , HOH B:1375 , FAD B:2805
BINDING SITE FOR RESIDUE FUM B 2806
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
[
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: MULTIHEME_CYTC (A:9-91,B:9-91,A:9-91,B:9-91)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
MULTIHEME_CYTC
PS51008
Multiheme cytochrome c family profile.
FRDA_SHEFR
9-91
2
A:9-91
B:9-91
FRDA_SHEFN
34-116
2
A:9-91
B:9-91
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(3, 6)
Info
All SCOP Domains
1a: SCOP_d1jrxa1 (A:1-102)
1b: SCOP_d1jrxb1 (B:1-102)
2a: SCOP_d1jrxa3 (A:360-505)
2b: SCOP_d1jrxb3 (B:360-505)
3a: SCOP_d1jrxa2 (A:103-359,A:506-568)
3b: SCOP_d1jrxb2 (B:103-359,B:506-568)
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)
Families
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Multiheme cytochromes
(149)
Superfamily
:
Multiheme cytochromes
(149)
Family
:
Di-heme elbow motif
(53)
Protein domain
:
Flavocytochrome c3 (respiratory fumarate reductase), N-terminal domain
(22)
Shewanella frigidimarina [TaxId: 56812]
(16)
1a
d1jrxa1
A:1-102
1b
d1jrxb1
B:1-102
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
(45)
Superfamily
:
Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
(45)
Family
:
Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
(45)
Protein domain
:
Flavocytochrome c3 (respiratory fumarate reductase)
(19)
Shewanella frigidimarina [TaxId: 56812]
(16)
2a
d1jrxa3
A:360-505
2b
d1jrxb3
B:360-505
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
FAD/NAD(P)-binding domain
(331)
Superfamily
:
FAD/NAD(P)-binding domain
(331)
Family
:
Succinate dehydrogenase/fumarate reductase flavoprotein N-terminal domain
(45)
Protein domain
:
Flavocytochrome c3 (respiratory fumarate reductase)
(19)
Shewanella frigidimarina [TaxId: 56812]
(16)
3a
d1jrxa2
A:103-359,A:506-568
3b
d1jrxb2
B:103-359,B:506-568
[
close SCOP info
]
CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_1jrxA03 (A:103-359,A:506-568)
1b: CATH_1jrxB03 (B:103-359,B:506-568)
2a: CATH_1jrxA01 (A:365-502)
2b: CATH_1jrxB01 (B:365-502)
3a: CATH_1jrxA02 (A:1-99)
3b: CATH_1jrxB02 (B:1-99)
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(bba) Sandwich
(528)
Topology
:
FAD/NAD(P)-binding domain
(373)
Homologous Superfamily
:
[code=3.50.50.60, no name defined]
(373)
Shewanella frigidimarina. Organism_taxid: 56812.
(13)
1a
1jrxA03
A:103-359,A:506-568
1b
1jrxB03
B:103-359,B:506-568
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Flavocytochrome C3; Chain A, domain 1
(40)
Homologous Superfamily
:
Flavocytochrome C3; Chain A, domain 1
(40)
Shewanella frigidimarina. Organism_taxid: 56812.
(13)
2a
1jrxA01
A:365-502
2b
1jrxB01
B:365-502
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Flavocytochrome C3; Chain A, domain 2
(23)
Homologous Superfamily
:
Flavocytochrome C3; Chain A
(23)
Shewanella frigidimarina. Organism_taxid: 56812.
(13)
3a
1jrxA02
A:1-99
3b
1jrxB02
B:1-99
[
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]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_FAD_binding_2_1jrxB01 (B:128-550)
1b: PFAM_FAD_binding_2_1jrxB02 (B:128-550)
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Clan
:
NADP_Rossmann
(1239)
Family
:
FAD_binding_2
(21)
Shewanella frigidimarina
(9)
1a
FAD_binding_2-1jrxB01
B:128-550
1b
FAD_binding_2-1jrxB02
B:128-550
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