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1H29
Biol. Unit 4
Info
Asym.Unit (409 KB)
Biol.Unit 1 (102 KB)
Biol.Unit 2 (101 KB)
Biol.Unit 3 (103 KB)
Biol.Unit 4 (100 KB)
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(1)
Title
:
SULFATE RESPIRATION IN DESULFOVIBRIO VULGARIS HILDENBOROUGH: STRUCTURE OF THE 16-HEME CYTOCHROME C HMCA AT 2.5 A RESOLUTION AND A VIEW OF ITS ROLE IN TRANSMEMBRANE ELECTRON TRANSFER
Authors
:
P. M. Matias, A. V. Coelho, F. M. A. Valente, D. Placido, J. Legall, A. V. Xavier, I. A. C. Pereira, M. A. Carrondo
Date
:
01 Aug 02 (Deposition) - 02 Oct 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.51
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
:
Electron Transport, High Molecular Mass Cytochrome, Sulfate Respiration, Hydrogen Cycle, Transmembrane Redox Complex, Energy Conservation, Proton Gradient, Tetra-Heme, C3-Like Domain
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. M. Matias, A. V. Coelho, F. M. A. Valente, D. Placido, J. Legall, A. V. Xavier, I. A. C. Pereira, M. A. Carrondo
Sulfate Respiration In Desulfovibrio Vulgaris Hildenborough: Structure Of The 16-Heme Cytochrome C Hmca At 2. 5 A Resolution And A View Of Its Role In Transmembrane Electron Transfer
J. Biol. Chem. V. 277 47907 2002
[
close entry info
]
Hetero Components
(1, 16)
Info
All Hetero Components
1a: HEME C (HECa)
1aa: HEME C (HECaa)
1ab: HEME C (HECab)
1ac: HEME C (HECac)
1ad: HEME C (HECad)
1ae: HEME C (HECae)
1af: HEME C (HECaf)
1ag: HEME C (HECag)
1ah: HEME C (HECah)
1ai: HEME C (HECai)
1aj: HEME C (HECaj)
1ak: HEME C (HECak)
1al: HEME C (HECal)
1am: HEME C (HECam)
1an: HEME C (HECan)
1ao: HEME C (HECao)
1ap: HEME C (HECap)
1aq: HEME C (HECaq)
1ar: HEME C (HECar)
1as: HEME C (HECas)
1at: HEME C (HECat)
1au: HEME C (HECau)
1av: HEME C (HECav)
1aw: HEME C (HECaw)
1ax: HEME C (HECax)
1ay: HEME C (HECay)
1az: HEME C (HECaz)
1b: HEME C (HECb)
1ba: HEME C (HECba)
1bb: HEME C (HECbb)
1bc: HEME C (HECbc)
1bd: HEME C (HECbd)
1be: HEME C (HECbe)
1bf: HEME C (HECbf)
1bg: HEME C (HECbg)
1bh: HEME C (HECbh)
1bi: HEME C (HECbi)
1bj: HEME C (HECbj)
1bk: HEME C (HECbk)
1bl: HEME C (HECbl)
1c: HEME C (HECc)
1d: HEME C (HECd)
1e: HEME C (HECe)
1f: HEME C (HECf)
1g: HEME C (HECg)
1h: HEME C (HECh)
1i: HEME C (HECi)
1j: HEME C (HECj)
1k: HEME C (HECk)
1l: HEME C (HECl)
1m: HEME C (HECm)
1n: HEME C (HECn)
1o: HEME C (HECo)
1p: HEME C (HECp)
1q: HEME C (HECq)
1r: HEME C (HECr)
1s: HEME C (HECs)
1t: HEME C (HECt)
1u: HEME C (HECu)
1v: HEME C (HECv)
1w: HEME C (HECw)
1x: HEME C (HECx)
1y: HEME C (HECy)
1z: HEME C (HECz)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
HEC
16
Ligand/Ion
HEME C
[
close Hetero Component info
]
Sites
(18, 18)
Info
All Sites
01: CC1 (SOFTWARE)
02: DC5 (SOFTWARE)
03: FC4 (SOFTWARE)
04: FC5 (SOFTWARE)
05: FC6 (SOFTWARE)
06: FC7 (SOFTWARE)
07: FC8 (SOFTWARE)
08: FC9 (SOFTWARE)
09: GC1 (SOFTWARE)
10: GC2 (SOFTWARE)
11: GC3 (SOFTWARE)
12: GC4 (SOFTWARE)
13: GC5 (SOFTWARE)
14: GC6 (SOFTWARE)
15: GC7 (SOFTWARE)
16: GC8 (SOFTWARE)
17: GC9 (SOFTWARE)
18: HC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
CC1
SOFTWARE
ILE B:48 , GLY B:49 , ALA B:50 , MET B:51 , LEU B:57 , ASP B:58 , LEU B:59 , VAL B:62 , LYS B:107 , TYR B:110 , HIS B:111 , GLN B:131 , ASP B:132 , GLU B:134 , CYS B:135 , CYS B:138 , HIS B:139 , HOH B:2110 , GLN D:517
BINDING SITE FOR RESIDUE HEC B1103
02
DC5
SOFTWARE
ILE B:435 , GLY B:436 , SER B:437 , ILE B:438 , ALA B:439 , LYS B:440 , GLU B:441 , TYR B:442 , SER B:445 , LYS B:512 , TYR B:515 , HIS B:516 , CYS B:519 , ALA B:532 , ASN B:533 , CYS B:536 , CYS B:539 , HIS B:540 , LYS D:123 , GLN D:131
BINDING SITE FOR RESIDUE HEC B1116
03
FC4
SOFTWARE
ILE D:46 , HIS D:66 , THR D:70 , CYS D:80 , CYS D:83 , HIS D:84 , LEU D:93 , LYS D:94 , PHE D:95 , ARG D:97 , TYR D:110 , HIS D:222 , ILE D:226 , MET D:230 , HEC D:1102 , HOH D:2108
BINDING SITE FOR RESIDUE HEC D1101
04
FC5
SOFTWARE
VAL D:62 , PHE D:64 , ARG D:65 , GLN D:68 , HIS D:69 , ALA D:72 , VAL D:73 , PHE D:95 , CYS D:114 , CYS D:117 , HIS D:118 , LEU D:121 , LYS D:127 , GLY D:129 , PRO D:130 , HEC D:1101
BINDING SITE FOR RESIDUE HEC D1102
05
FC6
SOFTWARE
GLN B:517 , ILE D:48 , GLY D:49 , ALA D:50 , MET D:51 , LEU D:57 , ASP D:58 , LEU D:59 , TYR D:110 , HIS D:111 , HIS D:118 , GLN D:131 , ASP D:132 , CYS D:135 , CYS D:138 , HIS D:139
BINDING SITE FOR RESIDUE HEC D1103
06
FC7
SOFTWARE
GLY D:153 , PHE D:154 , HIS D:159 , HIS D:162 , VAL D:163 , ASN D:177 , CYS D:178 , CYS D:181 , HIS D:182 , GLU D:199 , SER D:201 , ARG D:203 , LEU D:265 , ASP D:266 , ASP D:307 , CYS D:308 , ARG D:309 , ILE D:316 , HEC D:1105 , HEC D:1106 , HEC D:1108
BINDING SITE FOR RESIDUE HEC D1104
07
FC8
SOFTWARE
HIS D:183 , TYR D:185 , LEU D:192 , ASP D:200 , SER D:201 , CYS D:202 , CYS D:205 , HIS D:206 , LYS D:213 , ARG D:214 , PRO D:215 , ALA D:220 , ALA D:224 , HEC D:1104 , HOH D:2110
BINDING SITE FOR RESIDUE HEC D1105
08
FC9
SOFTWARE
PHE D:154 , ARG D:161 , HIS D:162 , SER D:165 , CYS D:225 , CYS D:228 , HIS D:229 , GLU D:238 , THR D:239 , GLY D:240 , PRO D:241 , PHE D:256 , HEC D:1104 , HEC D:1107 , HOH D:2032 , HOH D:2111
BINDING SITE FOR RESIDUE HEC D1106
09
GC1
SOFTWARE
ILE D:46 , HIS D:66 , TRP D:149 , GLU D:151 , ILE D:152 , ASP D:218 , ALA D:221 , HIS D:222 , CYS D:225 , ILE D:226 , VAL D:242 , ASN D:243 , CYS D:244 , CYS D:247 , HIS D:248 , HEC D:1106
BINDING SITE FOR RESIDUE HEC D1107
10
GC2
SOFTWARE
ARG D:267 , GLN D:269 , ILE D:275 , HIS D:298 , ALA D:305 , ASP D:307 , CYS D:308 , CYS D:311 , HIS D:312 , ILE D:316 , THR D:318 , CYS D:319 , THR D:320 , ARG D:406 , HEC D:1104 , HEC D:1110 , HOH D:2065
BINDING SITE FOR RESIDUE HEC D1108
11
GC3
SOFTWARE
CYS D:311 , HIS D:312 , HIS D:313 , THR D:318 , CYS D:319 , CYS D:322 , HIS D:323 , ASP D:330 , SER D:331 , LYS D:338 , ALA D:339 , GLN D:342 , SER D:345 , ARG D:347
BINDING SITE FOR RESIDUE HEC D1109
12
GC4
SOFTWARE
ILE D:275 , PHE D:296 , HIS D:301 , LYS D:304 , CYS D:311 , MET D:346 , ARG D:347 , SER D:348 , CYS D:349 , CYS D:352 , HIS D:353 , ARG D:356 , ARG D:417 , ASP D:463 , LYS D:464 , LEU D:465 , THR D:468 , HEC D:1108 , HEC D:1112
BINDING SITE FOR RESIDUE HEC D1110
13
GC5
SOFTWARE
VAL D:357 , CYS D:362 , CYS D:365 , HIS D:366 , ILE D:369 , PRO D:371 , THR D:372 , GLN D:377 , ASP D:463 , PHE D:469 , HIS D:470 , THR D:475 , LEU D:476 , GLN D:478 , GLY D:479
BINDING SITE FOR RESIDUE HEC D1111
14
GC6
SOFTWARE
GLU D:261 , ILE D:275 , PRO D:277 , GLY D:289 , THR D:290 , MET D:291 , LYS D:292 , PRO D:293 , VAL D:294 , LEU D:336 , MET D:340 , HIS D:341 , CYS D:349 , CYS D:378 , CYS D:381 , HIS D:382 , HEC D:1110
BINDING SITE FOR RESIDUE HEC D1112
15
GC7
SOFTWARE
ILE D:429 , ILE D:435 , PHE D:447 , HIS D:449 , VAL D:453 , CYS D:477 , CYS D:480 , HIS D:481 , SER D:487 , LEU D:488 , PRO D:490 , LYS D:492 , CYS D:493 , TYR D:515 , HEC D:1115
BINDING SITE FOR RESIDUE HEC D1113
16
GC8
SOFTWARE
PHE D:368 , LYS D:370 , CYS D:480 , HIS D:482 , ASN D:483 , CYS D:493 , CYS D:496 , HIS D:497 , ASP D:507 , ALA D:514 , GLN D:517 , GLN D:518
BINDING SITE FOR RESIDUE HEC D1114
17
GC9
SOFTWARE
SER D:445 , PHE D:447 , LYS D:451 , ILE D:452 , THR D:455 , CYS D:480 , GLN D:518 , CYS D:519 , CYS D:522 , HIS D:523 , LYS D:530 , HEC D:1113
BINDING SITE FOR RESIDUE HEC D1115
18
HC1
SOFTWARE
GLN B:131 , ILE D:435 , GLY D:436 , SER D:437 , ILE D:438 , ALA D:439 , LYS D:440 , GLU D:441 , TYR D:442 , LYS D:512 , TYR D:515 , HIS D:516 , CYS D:519 , MET D:520 , ALA D:532 , ASN D:533 , CYS D:536 , CYS D:539 , HIS D:540 , HOH D:2112
BINDING SITE FOR RESIDUE HEC D1116
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: MULTIHEME_CYTC (D:75-542)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
MULTIHEME_CYTC
PS51008
Multiheme cytochrome c family profile.
HMWC_DESVH
75-545
1
-
-
-
D:75-542
[
close PROSITE info
]
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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1h29a_ (A:)
1b: SCOP_d1h29b_ (B:)
1c: SCOP_d1h29c_ (C:)
1d: SCOP_d1h29d_ (D:)
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Multiheme cytochromes
(149)
Superfamily
:
Multiheme cytochromes
(149)
Family
:
Cytochrome c3-like
(70)
Protein domain
:
16-heme cytochrome c HmcA
(3)
Desulfovibrio vulgaris [TaxId: 881]
(3)
1a
d1h29a_
A:
1b
d1h29b_
B:
1c
d1h29c_
C:
1d
d1h29d_
D:
[
close SCOP info
]
CATH Domains
(1, 16)
Info
all CATH domains
1a: CATH_1h29A02 (A:149-258)
1b: CATH_1h29D01 (D:38-148)
1c: CATH_1h29B04 (B:421-541)
1d: CATH_1h29D04 (D:421-542)
1e: CATH_1h29A04 (A:421-543)
1f: CATH_1h29C04 (C:421-544)
1g: CATH_1h29D03 (D:270-420)
1h: CATH_1h29A03 (A:270-420)
1i: CATH_1h29B03 (B:270-420)
1j: CATH_1h29C03 (C:270-420)
1k: CATH_1h29B02 (B:149-258)
1l: CATH_1h29C02 (C:149-258)
1m: CATH_1h29D02 (D:149-258)
1n: CATH_1h29A01 (A:38-148)
1o: CATH_1h29B01 (B:38-148)
1p: CATH_1h29C01 (C:38-148)
View:
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(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Cytochrome C3
(62)
Homologous Superfamily
:
Cytochrome C3
(62)
Desulfovibrio vulgaris. Organism_taxid: 882. Strain: hildenborough
(3)
1a
1h29A02
A:149-258
1b
1h29D01
D:38-148
1c
1h29B04
B:421-541
1d
1h29D04
D:421-542
1e
1h29A04
A:421-543
1f
1h29C04
C:421-544
1g
1h29D03
D:270-420
1h
1h29A03
A:270-420
1i
1h29B03
B:270-420
1j
1h29C03
C:270-420
1k
1h29B02
B:149-258
1l
1h29C02
C:149-258
1m
1h29D02
D:149-258
1n
1h29A01
A:38-148
1o
1h29B01
B:38-148
1p
1h29C01
C:38-148
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Chain D
Asymmetric Unit 1
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Asym.Unit (409 KB)
Header - Asym.Unit
Biol.Unit 1 (102 KB)
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