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1D4C
Asym. Unit
Info
Asym.Unit (370 KB)
Biol.Unit 1 (95 KB)
Biol.Unit 2 (94 KB)
Biol.Unit 3 (95 KB)
Biol.Unit 4 (95 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE UNCOMPLEXED FORM OF THE FLAVOCYTOCHROME C FUMARATE REDUCTASE OF SHEWANELLA PUTREFACIENS STRAIN MR-1
Authors
:
D. Leys, A. S. Tsapin, T. E. Meyer, M. A. Cusanovich, J. J. Van Beeumen
Date
:
03 Oct 99 (Deposition) - 01 Dec 99 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.90
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Tetraheme Flavocytochrome C, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Leys, A. S. Tsapin, K. H. Nealson, T. E. Meyer, M. A. Cusanovich, J. J. Van Beeumen
Structure And Mechanism Of The Flavocytochrome C Fumarate Reductase Of Shewanella Putrefaciens Mr-1.
Nat. Struct. Biol. V. 6 1113 1999
(for further references see the
PDB file header
)
[
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]
Hetero Components
(3, 23)
Info
All Hetero Components
1a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
1b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
1c: FLAVIN-ADENINE DINUCLEOTIDE (FADc)
1d: FLAVIN-ADENINE DINUCLEOTIDE (FADd)
2a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
2b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
2c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
2d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
2e: PROTOPORPHYRIN IX CONTAINING FE (HEMe)
2f: PROTOPORPHYRIN IX CONTAINING FE (HEMf)
2g: PROTOPORPHYRIN IX CONTAINING FE (HEMg)
2h: PROTOPORPHYRIN IX CONTAINING FE (HEMh)
2i: PROTOPORPHYRIN IX CONTAINING FE (HEMi)
2j: PROTOPORPHYRIN IX CONTAINING FE (HEMj)
2k: PROTOPORPHYRIN IX CONTAINING FE (HEMk)
2l: PROTOPORPHYRIN IX CONTAINING FE (HEMl)
2m: PROTOPORPHYRIN IX CONTAINING FE (HEMm)
2n: PROTOPORPHYRIN IX CONTAINING FE (HEMn)
2o: PROTOPORPHYRIN IX CONTAINING FE (HEMo)
2p: PROTOPORPHYRIN IX CONTAINING FE (HEMp)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FAD
4
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
2
HEM
16
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
3
SO4
3
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(23, 23)
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)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG C:401 , HIS C:503 , ARG C:544 , GLY C:546 , GLY C:547 , FAD C:800
BINDING SITE FOR RESIDUE SO4 C 814
02
AC2
SOFTWARE
MET B:235 , MET B:374 , ARG B:401 , HIS B:503 , ARG B:544 , GLY B:546 , GLY B:547 , FAD B:700
BINDING SITE FOR RESIDUE SO4 B 714
03
AC3
SOFTWARE
ARG D:401 , HIS D:503 , ARG D:544 , GLY D:546 , GLY D:547 , FAD D:900
BINDING SITE FOR RESIDUE SO4 D 914
04
AC4
SOFTWARE
VAL A:57 , SER A:62 , HIS A:63 , LEU A:64 , TYR A:83 , CYS A:84 , CYS A:87 , HIS A:88 , PHE A:90 , LEU A:166 , HIS A:337 , VAL A:373 , GLY A:433 , TYR A:434 , LEU A:437 , HOH A:612
BINDING SITE FOR RESIDUE HEM A 601
05
AC5
SOFTWARE
HIS A:42 , LEU A:45 , LEU A:48 , PRO A:59 , HIS A:60 , ILE A:68 , ALA A:69 , CYS A:70 , CYS A:73 , HIS A:74 , ASP A:93 , MET A:94 , ILE C:202 , TYR C:360
BINDING SITE FOR RESIDUE HEM A 602
06
AC6
SOFTWARE
ALA A:6 , GLY A:14 , CYS A:15 , CYS A:18 , HIS A:19 , LYS A:23 , THR A:71 , LYS A:75 , GLY A:76 , HIS A:77 , TYR A:297 , HOH A:649
BINDING SITE FOR RESIDUE HEM A 603
07
AC7
SOFTWARE
PHE A:8 , HIS A:9 , MET A:12 , SER A:17 , GLN A:37 , CYS A:38 , CYS A:41 , HIS A:42 , HIS A:74 , PRO A:95 , ARG C:200 , LYS C:324 , TYR C:325 , GLU C:359 , TYR C:360
BINDING SITE FOR RESIDUE HEM A 604
08
AC8
SOFTWARE
GLY A:132 , GLY A:134 , ALA A:136 , LEU A:154 , GLU A:155 , LYS A:156 , GLU A:157 , GLY A:162 , ASN A:163 , THR A:164 , LEU A:166 , ALA A:167 , ALA A:168 , GLY A:169 , GLY A:170 , VAL A:277 , ALA A:312 , GLY A:313 , THR A:335 , ASN A:336 , HIS A:337 , ASP A:343 , HIS A:503 , HIS A:504 , GLY A:533 , GLU A:534 , ARG A:544 , GLY A:547 , ASN A:548 , ALA A:549 , ILE A:550 , ILE A:553 , HOH A:605 , HOH A:607 , HOH A:608 , HOH A:638
BINDING SITE FOR RESIDUE FAD A 600
09
AC9
SOFTWARE
SER B:58 , SER B:62 , HIS B:63 , LEU B:64 , TYR B:83 , CYS B:84 , CYS B:87 , HIS B:88 , PHE B:90 , LEU B:166 , ALA B:168 , VAL B:373 , GLY B:433 , TYR B:434 , LEU B:437 , HEM B:602
BINDING SITE FOR RESIDUE HEM B 601
10
BC1
SOFTWARE
HIS B:42 , GLY B:43 , LEU B:45 , LEU B:48 , PRO B:59 , HIS B:60 , ILE B:68 , ALA B:69 , CYS B:70 , CYS B:73 , HIS B:74 , ASP B:93 , MET B:94 , PRO B:95 , HEM B:601 , HEM B:604 , GLU D:359 , TYR D:360
BINDING SITE FOR RESIDUE HEM B 602
11
BC2
SOFTWARE
ALA B:6 , GLY B:14 , CYS B:15 , CYS B:18 , HIS B:19 , LYS B:23 , GLY B:24 , GLY B:25 , THR B:71 , LYS B:75 , GLY B:76 , HIS B:77 , TYR B:297
BINDING SITE FOR RESIDUE HEM B 603
12
BC3
SOFTWARE
LEU B:5 , PHE B:8 , HIS B:9 , SER B:17 , GLN B:37 , CYS B:38 , CYS B:41 , HIS B:42 , HIS B:74 , PRO B:95 , HEM B:602 , ARG D:200 , TYR D:325 , ASP D:326 , PRO D:327 , TYR D:360 , HOH D:925
BINDING SITE FOR RESIDUE HEM B 604
13
BC4
SOFTWARE
ILE B:131 , GLY B:132 , SER B:133 , GLY B:134 , ALA B:136 , GLU B:155 , LYS B:156 , GLU B:157 , GLY B:162 , ASN B:163 , THR B:164 , ALA B:167 , GLY B:169 , GLY B:170 , ARG B:276 , VAL B:277 , ALA B:312 , GLY B:313 , THR B:335 , ASN B:336 , HIS B:337 , ASP B:343 , MET B:374 , HIS B:503 , HIS B:504 , GLY B:533 , GLU B:534 , ARG B:544 , GLY B:547 , ASN B:548 , ALA B:549 , ILE B:550 , ILE B:553 , SO4 B:714 , HOH B:728 , HOH B:733
BINDING SITE FOR RESIDUE FAD B 700
14
BC5
SOFTWARE
SER C:58 , SER C:62 , HIS C:63 , LEU C:64 , TYR C:83 , CYS C:84 , CYS C:87 , HIS C:88 , PHE C:90 , LEU C:166 , ALA C:168 , HIS C:337 , VAL C:373 , GLY C:433 , TYR C:434 , HIS C:436 , LEU C:437
BINDING SITE FOR RESIDUE HEM C 601
15
BC6
SOFTWARE
TYR A:360 , HIS C:42 , GLY C:43 , LEU C:45 , LEU C:48 , PRO C:59 , HIS C:60 , ILE C:68 , ALA C:69 , CYS C:70 , CYS C:73 , HIS C:74 , ASP C:93 , MET C:94 , HEM C:604
BINDING SITE FOR RESIDUE HEM C 602
16
BC7
SOFTWARE
ALA C:6 , GLY C:14 , CYS C:15 , CYS C:18 , HIS C:19 , LYS C:23 , GLY C:24 , VAL C:26 , LYS C:75 , GLY C:76 , HIS C:77 , TYR C:297
BINDING SITE FOR RESIDUE HEM C 603
17
BC8
SOFTWARE
ARG A:200 , TYR A:325 , PRO A:327 , GLU A:359 , TYR A:360 , LEU C:5 , PHE C:8 , HIS C:9 , SER C:17 , GLN C:37 , CYS C:38 , CYS C:41 , HIS C:42 , HIS C:74 , HEM C:602
BINDING SITE FOR RESIDUE HEM C 604
18
BC9
SOFTWARE
ILE C:131 , GLY C:132 , GLY C:134 , GLY C:135 , ALA C:136 , LEU C:154 , GLU C:155 , LYS C:156 , GLY C:162 , ASN C:163 , THR C:164 , ALA C:167 , ALA C:168 , GLY C:169 , GLY C:170 , ARG C:276 , VAL C:277 , ALA C:312 , THR C:335 , ASN C:336 , HIS C:337 , ASP C:343 , MET C:374 , HIS C:503 , HIS C:504 , GLY C:533 , GLU C:534 , ARG C:544 , GLY C:547 , ASN C:548 , ALA C:549 , ILE C:550 , ILE C:553 , SO4 C:814 , HOH C:822 , HOH C:826 , HOH C:831 , HOH C:844
BINDING SITE FOR RESIDUE FAD C 800
19
CC1
SOFTWARE
VAL D:57 , SER D:58 , SER D:62 , HIS D:63 , LEU D:64 , TYR D:83 , CYS D:84 , CYS D:87 , HIS D:88 , LEU D:166 , ALA D:168 , HIS D:337 , VAL D:373 , GLY D:433 , LEU D:437
BINDING SITE FOR RESIDUE HEM D 601
20
CC2
SOFTWARE
TYR B:360 , HIS D:42 , LEU D:45 , LEU D:48 , PRO D:59 , HIS D:60 , ILE D:68 , ALA D:69 , CYS D:70 , CYS D:73 , HIS D:74 , ASP D:93 , MET D:94 , HEM D:604
BINDING SITE FOR RESIDUE HEM D 602
21
CC3
SOFTWARE
ALA D:6 , GLY D:14 , CYS D:15 , CYS D:18 , HIS D:19 , LYS D:23 , GLY D:24 , GLY D:25 , LEU D:31 , THR D:71 , LYS D:75 , GLY D:76 , HIS D:77 , TYR D:297 , HEM D:604
BINDING SITE FOR RESIDUE HEM D 603
22
CC4
SOFTWARE
ARG B:200 , TYR B:325 , ASP B:326 , TYR B:360 , LEU D:5 , PHE D:8 , HIS D:9 , MET D:12 , SER D:17 , GLN D:37 , CYS D:38 , CYS D:41 , HIS D:42 , HIS D:74 , HEM D:602 , HEM D:603
BINDING SITE FOR RESIDUE HEM D 604
23
CC5
SOFTWARE
ILE D:131 , GLY D:132 , GLY D:134 , GLY D:135 , ALA D:136 , GLU D:155 , LYS D:156 , GLU D:157 , GLY D:162 , ASN D:163 , THR D:164 , ALA D:167 , GLY D:169 , GLY D:170 , VAL D:277 , ALA D:312 , GLY D:313 , THR D:335 , ASN D:336 , HIS D:337 , ASP D:343 , HIS D:503 , HIS D:504 , GLY D:533 , GLU D:534 , ARG D:544 , GLY D:547 , ASN D:548 , ALA D:549 , ILE D:550 , ILE D:553 , SO4 D:914 , HOH D:921 , HOH D:922 , HOH D:923 , HOH D:924 , HOH D:931
BINDING SITE FOR RESIDUE FAD D 900
[
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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, 4)
Info
All PROSITE Patterns/Profiles
1: MULTIHEME_CYTC (A:10-93,B:10-93,C:10-93,D:10-93)
;
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_SHEON
35-118
4
A:10-93
B:10-93
C:10-93
D:10-93
[
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]
Exons
(0, 0)
Info
All Exons
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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, 12)
Info
All SCOP Domains
1a: SCOP_d1d4ca1 (A:1-102)
1b: SCOP_d1d4cb1 (B:3-102)
1c: SCOP_d1d4cc1 (C:3-102)
1d: SCOP_d1d4cd1 (D:1-102)
2a: SCOP_d1d4ca3 (A:360-505)
2b: SCOP_d1d4cb3 (B:360-505)
2c: SCOP_d1d4cc3 (C:360-505)
2d: SCOP_d1d4cd3 (D:360-505)
3a: SCOP_d1d4ca2 (A:103-359,A:506-570)
3b: SCOP_d1d4cb2 (B:103-359,B:506-570)
3c: SCOP_d1d4cc2 (C:103-359,C:506-570)
3d: SCOP_d1d4cd2 (D:103-359,D:506-570)
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(
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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 putrefaciens [TaxId: 24]
(3)
1a
d1d4ca1
A:1-102
1b
d1d4cb1
B:3-102
1c
d1d4cc1
C:3-102
1d
d1d4cd1
D: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 putrefaciens [TaxId: 24]
(3)
2a
d1d4ca3
A:360-505
2b
d1d4cb3
B:360-505
2c
d1d4cc3
C:360-505
2d
d1d4cd3
D: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 putrefaciens [TaxId: 24]
(3)
3a
d1d4ca2
A:103-359,A:506-570
3b
d1d4cb2
B:103-359,B:506-570
3c
d1d4cc2
C:103-359,C:506-570
3d
d1d4cd2
D:103-359,D:506-570
[
close SCOP info
]
CATH Domains
(3, 12)
Info
all CATH domains
1a: CATH_1d4cA02 (A:103-360,A:508-566)
1b: CATH_1d4cB02 (B:103-360,B:508-566)
1c: CATH_1d4cC02 (C:103-360,C:508-566)
1d: CATH_1d4cD02 (D:103-360,D:508-566)
2a: CATH_1d4cA03 (A:361-505)
2b: CATH_1d4cB03 (B:361-505)
2c: CATH_1d4cC03 (C:361-505)
2d: CATH_1d4cD03 (D:361-505)
3a: CATH_1d4cB01 (B:3-102)
3b: CATH_1d4cC01 (C:3-102)
3c: CATH_1d4cA01 (A:1-102)
3d: CATH_1d4cD01 (D:1-102)
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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 oneidensis. Organism_taxid: 70863. Strain: mr1
(1)
1a
1d4cA02
A:103-360,A:508-566
1b
1d4cB02
B:103-360,B:508-566
1c
1d4cC02
C:103-360,C:508-566
1d
1d4cD02
D:103-360,D:508-566
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Flavocytochrome C3; Chain A, domain 1
(40)
Homologous Superfamily
:
Flavocytochrome C3; Chain A, domain 1
(40)
Shewanella oneidensis. Organism_taxid: 70863. Strain: mr1
(1)
2a
1d4cA03
A:361-505
2b
1d4cB03
B:361-505
2c
1d4cC03
C:361-505
2d
1d4cD03
D:361-505
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Flavocytochrome C3; Chain A, domain 2
(23)
Homologous Superfamily
:
Flavocytochrome C3; Chain A
(23)
Shewanella oneidensis. Organism_taxid: 70863. Strain: mr1
(1)
3a
1d4cB01
B:3-102
3b
1d4cC01
C:3-102
3c
1d4cA01
A:1-102
3d
1d4cD01
D:1-102
[
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Pfam Domains
(0, 0)
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