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3GM6
Biol. Unit 1
Info
Asym.Unit (328 KB)
Biol.Unit 1 (927 KB)
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(1)
Title
:
STRUCTURE OF THE THIOALKALIVIBRIO NITRATIREDUCENS CYTOCHROME C NITRITE REDUCTASE IN COMPLEX WITH PHOSPHATE
Authors
:
A. A. Trofimov, K. M. Polyakov, K. M. Boyko, A. A. Filimonenkov, P. V. Dorovatovsky, T. V. Tikhonova, V. O. Popov
Date
:
13 Mar 09 (Deposition) - 04 Aug 09 (Release) - 06 Oct 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (3x)
Keywords
:
Alpha Protein, Eight Hemes C, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. A. Trofimov, K. M. Polyakov, K. M. Boiko, A. A. Filimonenkov, P. V. Dorovatovskii, T. V. Tikhonova, V. O. Popov, M. V. Koval'Chuk
Structure Of Octaheme Cytochrome C Nitrite Reductase From Thioalkalivibrio Nitratireducens In A Complex With Phosphat
Crystallography Reports V. 55 58 2010
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Hetero Components
(4, 66)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
2a: HEME C (HECa)
2b: HEME C (HECb)
2c: HEME C (HECc)
2d: HEME C (HECd)
2e: HEME C (HECe)
2f: HEME C (HECf)
2g: HEME C (HECg)
2h: HEME C (HECh)
2i: HEME C (HECi)
2j: HEME C (HECj)
2k: HEME C (HECk)
2l: HEME C (HECl)
2m: HEME C (HECm)
2n: HEME C (HECn)
2o: HEME C (HECo)
2p: HEME C (HECp)
3a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
3b: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDb)
3c: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDc)
4a: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDa)
5a: PHOSPHATE ION (PO4a)
5b: PHOSPHATE ION (PO4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
HEC
48
Ligand/Ion
HEME C
3
MPD
9
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
4
MRD
3
Ligand/Ion
(4R)-2-METHYLPENTANE-2,4-DIOL
5
PO4
6
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
]
Sites
(24, 24)
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)
24: CC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:113 , ALA A:114 , ASP A:125 , HIS A:126 , VAL A:129 , ARG A:131 , CYS A:184 , CYS A:187 , LYS A:188 , ARG A:242 , CYS A:299 , HIS A:300 , TYR A:303 , HIS A:361 , ASN A:486 , PO4 A:526 , HOH A:545 , HOH A:713 , HOH A:714 , HOH A:720 , HEC A:1006
BINDING SITE FOR RESIDUE HEC A 1004
02
AC2
SOFTWARE
HIS A:70 , GLN A:73 , LEU A:225 , CYS A:227 , CYS A:230 , HIS A:231 , MET A:384 , LYS A:386 , TYR A:395 , THR A:396 , HIS A:398 , HOH A:818 , HOH A:846 , HEC A:1003
BINDING SITE FOR RESIDUE HEC A 1005
03
AC3
SOFTWARE
SER A:84 , PRO A:116 , ARG A:117 , HIS A:119 , PHE A:121 , MET A:122 , ASP A:125 , CYS A:187 , LYS A:188 , LEU A:225 , MET A:229 , CYS A:296 , CYS A:299 , HIS A:300 , HIS A:383 , MET A:384 , GLN A:400 , HOH A:534 , HOH A:551 , HOH A:553 , HOH A:708 , HEC A:1004 , HEC A:1007
BINDING SITE FOR RESIDUE HEC A 1006
04
AC4
SOFTWARE
PHE A:367 , HIS A:372 , ALA A:378 , CYS A:379 , CYS A:382 , HIS A:383 , THR A:402 , ARG A:404 , LYS A:431 , ASN A:486 , PHE A:490 , HIS A:491 , HOH A:551 , HOH A:708 , HOH A:709 , HOH A:710 , HOH A:717 , HOH A:721 , HEC A:1006
BINDING SITE FOR RESIDUE HEC A 1007
05
AC5
SOFTWARE
ASN A:141 , TRP A:142 , GLN A:143 , VAL A:371 , HIS A:372 , PRO A:403 , ALA A:410 , CYS A:411 , CYS A:414 , HIS A:415 , TRP A:418 , ILE A:427 , HOH A:652
BINDING SITE FOR RESIDUE HEC A 1008
06
AC6
SOFTWARE
CYS A:14 , PHE A:15 , HIS A:18 , HIS A:25 , VAL A:33 , ASN A:34 , CYS A:35 , CYS A:38 , HIS A:39 , LEU A:194 , PHE A:228 , PRO A:233 , HIS A:234 , ARG A:239 , PHE A:274 , ARG A:276 , ARG A:282 , HOH A:643 , HOH A:680 , HOH A:984 , HEC A:1001 , HEC A:1003
BINDING SITE FOR RESIDUE HEC A 1002
07
AC7
SOFTWARE
LYS A:29 , HIS A:30 , HIS A:37 , ALA A:65 , CYS A:66 , THR A:68 , CYS A:69 , HIS A:70 , HIS A:231 , ALA A:236 , HOH A:905 , HEC A:1002 , HEC A:1005 , HOH A:1030 , HOH A:1040
BINDING SITE FOR RESIDUE HEC A 1003
08
AC8
SOFTWARE
GLN A:13 , CYS A:14 , CYS A:17 , HIS A:18 , HIS A:39 , HIS A:44 , ALA A:48 , SER A:49 , SER A:50 , ARG A:52 , ARG A:56 , PRO A:57 , THR A:59 , LEU A:194 , ARG A:276 , GLY A:277 , HOH A:646 , HOH A:685 , HOH A:973 , HOH A:982 , HEC A:1002
BINDING SITE FOR RESIDUE HEC A 1001
09
AC9
SOFTWARE
PHE A:109 , ARG A:131 , TYR A:303 , GLN A:360 , HIS A:361 , HOH A:715 , HOH A:720 , HOH A:732 , HEC A:1004
BINDING SITE FOR RESIDUE PO4 A 526
10
BC1
SOFTWARE
GLU A:302 , TYR A:303 , LYS A:358 , GLN A:360 , HOH A:821 , HOH A:822
BINDING SITE FOR RESIDUE CA A 527
11
BC2
SOFTWARE
ARG A:87 , GLN A:138 , PHE A:139 , TRP A:142 , ARG A:497 , HOH A:910
BINDING SITE FOR RESIDUE MPD A 528
12
BC3
SOFTWARE
LYS A:431 , ASN A:432 , HIS A:435
BINDING SITE FOR RESIDUE MPD A 529
13
BC4
SOFTWARE
HIS B:113 , ALA B:114 , ASP B:125 , HIS B:126 , VAL B:129 , ARG B:131 , CYS B:184 , CYS B:187 , LYS B:188 , ARG B:242 , CYS B:299 , HIS B:300 , TYR B:303 , HIS B:361 , ASN B:486 , PO4 B:526 , HOH B:620 , HOH B:766 , HOH B:767 , HOH B:773 , HEC B:1006
BINDING SITE FOR RESIDUE HEC B 1004
14
BC5
SOFTWARE
HIS B:70 , GLN B:73 , LEU B:225 , CYS B:227 , CYS B:230 , HIS B:231 , MET B:384 , TYR B:395 , THR B:396 , HIS B:398 , HOH B:583 , HOH B:871 , HOH B:899 , HEC B:1003 , HOH B:1053
BINDING SITE FOR RESIDUE HEC B 1005
15
BC6
SOFTWARE
SER B:84 , PRO B:116 , ARG B:117 , HIS B:119 , PHE B:121 , MET B:122 , ASP B:125 , CYS B:187 , MET B:229 , CYS B:296 , CYS B:299 , HIS B:300 , HIS B:383 , MET B:384 , HOH B:609 , HOH B:627 , HOH B:629 , HOH B:761 , HEC B:1004 , HEC B:1007
BINDING SITE FOR RESIDUE HEC B 1006
16
BC7
SOFTWARE
PHE B:367 , HIS B:372 , ALA B:378 , CYS B:379 , CYS B:382 , HIS B:383 , THR B:402 , ARG B:404 , LYS B:431 , ASN B:486 , PHE B:490 , HIS B:491 , HOH B:627 , HOH B:761 , HOH B:762 , HOH B:763 , HOH B:770 , HOH B:774 , HEC B:1006
BINDING SITE FOR RESIDUE HEC B 1007
17
BC8
SOFTWARE
ASN B:141 , TRP B:142 , GLN B:143 , VAL B:371 , HIS B:372 , PRO B:403 , ALA B:410 , CYS B:411 , CYS B:414 , HIS B:415 , TRP B:418 , ILE B:427 , HOH B:555
BINDING SITE FOR RESIDUE HEC B 1008
18
BC9
SOFTWARE
CYS B:14 , PHE B:15 , HIS B:18 , ILE B:21 , HIS B:25 , VAL B:33 , ASN B:34 , CYS B:35 , CYS B:38 , HIS B:39 , LEU B:194 , PHE B:228 , PRO B:233 , HIS B:234 , ARG B:239 , PHE B:274 , ARG B:276 , ARG B:282 , HOH B:699 , HOH B:733 , HEC B:1001 , HEC B:1003
BINDING SITE FOR RESIDUE HEC B 1002
19
CC1
SOFTWARE
THR A:68 , LYS B:29 , HIS B:30 , HIS B:37 , ALA B:65 , CYS B:66 , CYS B:69 , HIS B:70 , CYS B:227 , HIS B:231 , ALA B:236 , HOH B:534 , HOH B:573 , HOH B:598 , HOH B:959 , HEC B:1002 , HEC B:1005 , HOH B:1059
BINDING SITE FOR RESIDUE HEC B 1003
20
CC2
SOFTWARE
GLN B:13 , CYS B:14 , CYS B:17 , HIS B:18 , HIS B:39 , HIS B:44 , VAL B:45 , ALA B:48 , SER B:49 , ARG B:51 , ARG B:52 , MET B:53 , ARG B:56 , PRO B:57 , THR B:59 , LEU B:194 , GLN B:275 , ARG B:276 , HOH B:702 , HOH B:733 , HOH B:738 , HOH B:916 , HOH B:917 , HEC B:1002 , HOH B:1037 , HOH B:1046
BINDING SITE FOR RESIDUE HEC B 1001
21
CC3
SOFTWARE
PHE B:109 , ARG B:131 , TYR B:303 , GLN B:360 , HIS B:361 , HOH B:768 , HOH B:773 , HOH B:785 , HEC B:1004
BINDING SITE FOR RESIDUE PO4 B 526
22
CC4
SOFTWARE
GLU B:302 , TYR B:303 , LYS B:358 , GLN B:360 , HOH B:874 , HOH B:875
BINDING SITE FOR RESIDUE CA B 527
23
CC5
SOFTWARE
ARG B:87 , GLN B:138 , PHE B:139 , TRP B:142 , ARG B:497 , HOH B:964
BINDING SITE FOR RESIDUE MPD B 528
24
CC6
SOFTWARE
SER B:95 , LYS B:431 , HIS B:435 , HOH B:556 , HOH B:1065
BINDING SITE FOR RESIDUE MRD B 529
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 6)
Info
All PROSITE Patterns/Profiles
1: MULTIHEME_CYTC (A:9-420,B:9-420)
;
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.
NIR_THIND
37-448
6
A:9-420
B:9-420
[
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(0, 0)
Info
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Sorry, no Info available
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
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Info
all PFAM domains
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Sorry, no Info available
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Atom Selection
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)
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Protein & NOT Site
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select residue range 5 to 10 in chain 'A'
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show SS bonds with a radius of 100 units (=0.4Å)
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