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1H29
Biol. Unit 3
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
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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
(19, 19)
Info
All Sites
01: AC3 (SOFTWARE)
02: BC3 (SOFTWARE)
03: BC7 (SOFTWARE)
04: DC6 (SOFTWARE)
05: DC7 (SOFTWARE)
06: DC8 (SOFTWARE)
07: DC9 (SOFTWARE)
08: EC1 (SOFTWARE)
09: EC2 (SOFTWARE)
10: EC3 (SOFTWARE)
11: EC4 (SOFTWARE)
12: EC5 (SOFTWARE)
13: EC6 (SOFTWARE)
14: EC7 (SOFTWARE)
15: EC8 (SOFTWARE)
16: EC9 (SOFTWARE)
17: FC1 (SOFTWARE)
18: FC2 (SOFTWARE)
19: FC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC3
SOFTWARE
ILE A:48 , GLY A:49 , ALA A:50 , MET A:51 , LEU A:57 , ASP A:58 , LEU A:59 , VAL A:62 , TYR A:110 , HIS A:111 , HIS A:118 , GLN A:131 , ASP A:132 , CYS A:135 , CYS A:138 , HIS A:139 , HOH A:2118 , GLN C:517
BINDING SITE FOR RESIDUE HEC A1103
02
BC3
SOFTWARE
ILE A:275 , PRO A:277 , THR A:290 , MET A:291 , LYS A:292 , PRO A:293 , VAL A:294 , LEU A:336 , GLU A:337 , MET A:340 , HIS A:341 , CYS A:349 , CYS A:378 , CYS A:381 , HIS A:382 , HEC A:1110 , GLU C:261
BINDING SITE FOR RESIDUE HEC A1112
03
BC7
SOFTWARE
ILE A:435 , GLY A:436 , ILE A:438 , ALA A:439 , LYS A:440 , GLU A:441 , TYR A:442 , TYR A:515 , HIS A:516 , CYS A:519 , MET A:520 , ALA A:532 , ALA A:535 , CYS A:536 , CYS A:539 , HIS A:540 , HEC A:1115 , ALA C:122 , LYS C:123 , GLN C:131
BINDING SITE FOR RESIDUE HEC A1116
04
DC6
SOFTWARE
ILE C:46 , HIS C:66 , THR C:70 , CYS C:80 , CYS C:83 , HIS C:84 , LEU C:93 , LYS C:94 , PHE C:95 , ARG C:97 , TYR C:110 , ASP C:218 , HIS C:222 , HEC C:1102 , HEC C:1107
BINDING SITE FOR RESIDUE HEC C1101
05
DC7
SOFTWARE
ILE C:48 , VAL C:62 , PHE C:64 , ARG C:65 , GLN C:68 , HIS C:69 , ALA C:72 , CYS C:114 , CYS C:117 , HIS C:118 , LEU C:121 , LYS C:127 , GLY C:129 , PRO C:130 , HEC C:1101
BINDING SITE FOR RESIDUE HEC C1102
06
DC8
SOFTWARE
GLN A:517 , ILE C:48 , GLY C:49 , ALA C:50 , MET C:51 , LEU C:57 , ASP C:58 , LEU C:59 , VAL C:62 , LYS C:107 , TYR C:110 , HIS C:111 , ILE C:115 , HIS C:118 , GLN C:131 , ASP C:132 , CYS C:135 , CYS C:138 , HIS C:139 , HOH C:2125 , HOH C:2126
BINDING SITE FOR RESIDUE HEC C1103
07
DC9
SOFTWARE
GLY C:153 , PHE C:154 , HIS C:159 , HIS C:162 , ASN C:177 , CYS C:178 , CYS C:181 , HIS C:182 , GLU C:199 , SER C:201 , CYS C:202 , ARG C:203 , ASP C:266 , ASP C:307 , CYS C:308 , ARG C:309 , HEC C:1105 , HEC C:1106 , HOH C:2128
BINDING SITE FOR RESIDUE HEC C1104
08
EC1
SOFTWARE
HIS C:183 , TYR C:185 , LEU C:192 , ASP C:200 , SER C:201 , CYS C:202 , CYS C:205 , HIS C:206 , LYS C:213 , ARG C:214 , PRO C:215 , ALA C:220 , THR C:223 , ALA C:224 , HEC C:1104 , HOH C:2045 , HOH C:2129
BINDING SITE FOR RESIDUE HEC C1105
09
EC2
SOFTWARE
PHE C:154 , LEU C:158 , ARG C:161 , HIS C:162 , SER C:165 , ILE C:168 , CYS C:181 , ALA C:224 , CYS C:225 , CYS C:228 , HIS C:229 , GLU C:238 , THR C:239 , GLY C:240 , PRO C:241 , PHE C:256 , LYS C:257 , HEC C:1104 , HEC C:1107 , HOH C:2041 , HOH C:2131
BINDING SITE FOR RESIDUE HEC C1106
10
EC3
SOFTWARE
ILE C:46 , HIS C:66 , TRP C:149 , GLU C:151 , ILE C:152 , ALA C:221 , HIS C:222 , PRO C:241 , VAL C:242 , ASN C:243 , CYS C:244 , CYS C:247 , HIS C:248 , HEC C:1101 , HEC C:1106
BINDING SITE FOR RESIDUE HEC C1107
11
EC4
SOFTWARE
GLN C:269 , PRO C:270 , ILE C:275 , PHE C:296 , HIS C:298 , ALA C:305 , ASP C:307 , CYS C:308 , CYS C:311 , HIS C:312 , ILE C:316 , THR C:318 , CYS C:319 , THR C:320 , ARG C:406 , HEC C:1110 , HOH C:2132
BINDING SITE FOR RESIDUE HEC C1108
12
EC5
SOFTWARE
CYS C:311 , HIS C:312 , HIS C:313 , VAL C:314 , ARG C:315 , THR C:318 , CYS C:319 , CYS C:322 , HIS C:323 , ASP C:330 , LYS C:338 , ALA C:339 , GLN C:342 , SER C:345 , ARG C:347 , HOH C:2133
BINDING SITE FOR RESIDUE HEC C1109
13
EC6
SOFTWARE
PHE C:296 , HIS C:301 , LYS C:304 , CYS C:311 , MET C:346 , ARG C:347 , SER C:348 , CYS C:349 , CYS C:352 , HIS C:353 , ARG C:356 , ARG C:417 , LYS C:464 , LEU C:465 , THR C:468 , HEC C:1108
BINDING SITE FOR RESIDUE HEC C1110
14
EC7
SOFTWARE
VAL C:357 , GLN C:359 , THR C:361 , CYS C:362 , CYS C:365 , HIS C:366 , ILE C:369 , PRO C:371 , THR C:372 , GLN C:377 , LEU C:456 , ILE C:460 , ASP C:463 , LEU C:465 , PHE C:469 , HIS C:470 , THR C:475 , LEU C:476 , GLN C:478 , GLY C:479 , HOH C:2085 , HOH C:2134
BINDING SITE FOR RESIDUE HEC C1111
15
EC8
SOFTWARE
GLU B:261 , ILE C:275 , PRO C:277 , GLY C:289 , THR C:290 , MET C:291 , LYS C:292 , VAL C:294 , LEU C:336 , GLU C:337 , MET C:340 , HIS C:341 , CYS C:349 , CYS C:378 , CYS C:381 , HIS C:382 , HOH C:2072
BINDING SITE FOR RESIDUE HEC C1112
16
EC9
SOFTWARE
THR C:423 , ILE C:429 , PRO C:430 , ILE C:435 , PHE C:447 , HIS C:449 , ILE C:452 , VAL C:453 , CYS C:477 , CYS C:480 , HIS C:481 , SER C:487 , LEU C:488 , PRO C:490 , LYS C:492 , CYS C:493 , TYR C:515 , GLN C:518 , HEC C:1115
BINDING SITE FOR RESIDUE HEC C1113
17
FC1
SOFTWARE
PHE C:368 , LYS C:370 , HIS C:482 , ASN C:483 , PRO C:491 , CYS C:493 , SER C:495 , CYS C:496 , HIS C:497 , ARG C:508 , ALA C:514 , GLN C:517 , GLN C:518 , HOH C:2136
BINDING SITE FOR RESIDUE HEC C1114
18
FC2
SOFTWARE
SER C:445 , PHE C:447 , PRO C:448 , ILE C:452 , THR C:455 , GLN C:518 , CYS C:519 , CYS C:522 , HIS C:523 , MET C:526 , LYS C:530 , PRO C:531 , CYS C:539 , HEC C:1113 , HEC C:1116
BINDING SITE FOR RESIDUE HEC C1115
19
FC3
SOFTWARE
THR A:119 , GLN A:131 , ILE C:435 , GLY C:436 , SER C:437 , ILE C:438 , ALA C:439 , LYS C:440 , GLU C:441 , TYR C:442 , LYS C:512 , TYR C:515 , HIS C:516 , CYS C:519 , MET C:520 , HIS C:523 , ALA C:532 , ASN C:533 , CYS C:536 , CYS C:539 , HIS C:540 , HEC C:1115 , HOH C:2107
BINDING SITE FOR RESIDUE HEC C1116
[
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]
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 (C:75-544)
;
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
-
-
C:75-544
-
[
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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(
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(
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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
:
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
(
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(
)
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
[
close CATH info
]
Pfam Domains
(0, 0)
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all PFAM domains
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Asymmetric Unit 1
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