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3Q6J
Asym. Unit
Info
Asym.Unit (196 KB)
Biol.Unit 1 (190 KB)
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(1)
Title
:
STRUCTURAL BASIS FOR CARBON DIOXIDE BINDING BY 2-KETOPROPYL COENZYME M OXIDOREDUCTASE/CARBOXYLASE
Authors
:
A. S. Pandey, D. W. Mulder, S. A. Ensign, J. W. Peters
Date
:
01 Jan 11 (Deposition) - 16 Feb 11 (Release) - 16 Feb 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.92
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Disulfide, Carbon Dioxide, Coenzyme M, Fad, Nadp, Oxidoreductase, Carboxylase
(Keyword Search:
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Reference
:
A. S. Pandey, D. W. Mulder, S. A. Ensign, J. W. Peters
Structural Basis For Carbon Dioxide Binding By 2-Ketopropyl Coenzyme M Oxidoreductase/Carboxylase.
Febs Lett. V. 585 459 2011
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Hetero Components
(8, 12)
Info
All Hetero Components
1a: ACETONE (ACNa)
2a: BICARBONATE ION (BCTa)
2b: BICARBONATE ION (BCTb)
3a: CARBON DIOXIDE (CO2a)
4a: 1-THIOETHANESULFONIC ACID (COMa)
5a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
5b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
6a: (2-[2-KETOPROPYLTHIO]ETHANESULFONA... (KPCa)
7a: MAGNESIUM ION (MGa)
7b: MAGNESIUM ION (MGb)
8a: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPa)
8b: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACN
1
Ligand/Ion
ACETONE
2
BCT
2
Ligand/Ion
BICARBONATE ION
3
CO2
1
Ligand/Ion
CARBON DIOXIDE
4
COM
1
Ligand/Ion
1-THIOETHANESULFONIC ACID
5
FAD
2
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
6
KPC
1
Ligand/Ion
(2-[2-KETOPROPYLTHIO]ETHANESULFONATE
7
MG
2
Ligand/Ion
MAGNESIUM ION
8
NAP
2
Ligand/Ion
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
[
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Sites
(12, 12)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:90 , LEU A:189 , GLY A:222 , SER A:223 , LYS A:224 , THR A:225 , GLU A:228 , ARG A:245 , THR A:246 , LYS A:250 , GLY A:311 , LEU A:312 , GLY A:313 , MET A:359 , GLU A:360 , HOH A:567 , HOH A:634 , HOH A:667 , HOH A:672 , HOH A:742 , HOH A:951 , HOH A:952 , HOH A:954 , HOH A:960 , FAD A:1013
BINDING SITE FOR RESIDUE NAP A 1526
02
AC2
SOFTWARE
GLY A:50 , GLY A:52 , ALA A:53 , ALA A:54 , ASP A:73 , ARG A:74 , TRP A:75 , GLY A:80 , SER A:81 , ALA A:86 , CYS A:87 , HIS A:90 , HIS A:91 , PRO A:157 , ALA A:158 , ALA A:181 , VAL A:182 , GLY A:183 , HIS A:202 , TYR A:229 , GLY A:352 , ASP A:353 , MET A:359 , GLU A:360 , MET A:361 , ALA A:364 , HOH A:532 , HOH A:544 , HOH A:558 , HOH A:563 , HOH A:595 , HOH A:679 , HOH A:871 , HOH A:907 , HOH A:961 , NAP A:1526 , PHE B:501
BINDING SITE FOR RESIDUE FAD A 1013
03
AC3
SOFTWARE
LEU A:431 , BCT B:524 , COM B:525
BINDING SITE FOR RESIDUE ACN B 1040
04
AC4
SOFTWARE
ALA A:53 , ARG A:56 , PHE A:57 , GLY A:79 , CYS A:82 , PRO A:83 , MET A:140 , MET A:361 , ARG A:365 , BCT A:524 , HOH A:599 , CO2 A:1090 , LEU B:431
BINDING SITE FOR RESIDUE KPC A 526
05
AC5
SOFTWARE
LEU A:427 , VAL A:429 , LEU A:431 , ALA A:447 , SER A:450 , HOH A:686
BINDING SITE FOR RESIDUE MG A 527
06
AC6
SOFTWARE
LEU A:431 , PHE A:501 , HIS A:506 , GLN A:509 , ARG B:365 , HOH B:599 , HOH B:819 , ACN B:1040
BINDING SITE FOR RESIDUE BCT B 524
07
AC7
SOFTWARE
ARG A:365 , KPC A:526 , HOH A:599 , HOH A:697 , HOH A:735 , LEU B:431 , PHE B:501 , HIS B:506 , GLN B:509
BINDING SITE FOR RESIDUE BCT A 524
08
AC8
SOFTWARE
HIS B:90 , GLY B:222 , SER B:223 , LYS B:224 , THR B:225 , GLU B:228 , ARG B:245 , THR B:246 , LYS B:250 , GLY B:311 , LEU B:312 , GLY B:313 , GLU B:314 , MET B:359 , GLU B:360 , PHE B:390 , HOH B:556 , HOH B:615 , HOH B:655 , HOH B:662 , HOH B:775 , HOH B:840 , HOH B:903 , HOH B:926 , HOH B:981 , HOH B:999 , HOH B:1003 , HOH B:1006 , FAD B:1014
BINDING SITE FOR RESIDUE NAP B 1526
09
AC9
SOFTWARE
PHE A:501 , HOH A:566 , GLY B:50 , GLY B:52 , ALA B:53 , ALA B:54 , VAL B:72 , ASP B:73 , ARG B:74 , TRP B:75 , GLY B:80 , SER B:81 , ALA B:86 , CYS B:87 , HIS B:90 , HIS B:91 , PRO B:157 , ALA B:158 , ALA B:181 , VAL B:182 , GLY B:183 , HIS B:202 , TYR B:229 , GLY B:352 , ASP B:353 , MET B:359 , GLU B:360 , MET B:361 , ALA B:364 , PHE B:390 , HOH B:545 , HOH B:598 , HOH B:603 , HOH B:607 , HOH B:665 , HOH B:721 , HOH B:936 , HOH B:969 , NAP B:1526
BINDING SITE FOR RESIDUE FAD B 1014
10
BC1
SOFTWARE
ARG B:56 , PHE B:57 , GLY B:79 , CYS B:82 , PRO B:83 , MET B:140 , MET B:361 , ARG B:365 , ACN B:1040
BINDING SITE FOR RESIDUE COM B 525
11
BC2
SOFTWARE
PRO A:136 , KPC A:526 , HOH A:735 , ALA B:430 , LEU B:431
BINDING SITE FOR RESIDUE CO2 A 1090
12
BC3
SOFTWARE
LEU B:427 , VAL B:429 , LEU B:431 , ALA B:447 , SER B:450 , HOH B:574
BINDING SITE FOR RESIDUE MG B 527
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
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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
(2, 6)
Info
All SCOP Domains
1a: SCOP_d3q6ja3 (A:384-523)
1b: SCOP_d3q6jb3 (B:384-523)
2a: SCOP_d3q6ja1 (A:2-192,A:314-383)
2b: SCOP_d3q6ja2 (A:193-313)
2c: SCOP_d3q6jb1 (B:2-192,B:314-383)
2d: SCOP_d3q6jb2 (B:193-313)
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Protein Domains
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(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
CO dehydrogenase flavoprotein C-domain-like
(111)
Superfamily
:
FAD/NAD-linked reductases, dimerisation (C-terminal) domain
(76)
Family
:
FAD/NAD-linked reductases, dimerisation (C-terminal) domain
(76)
Protein domain
:
NADH-dependent 2-ketopropyl coenzyme M oxidoreductase/carboxylase
(5)
Xanthobacter sp., py2 [TaxId: 35809]
(5)
1a
d3q6ja3
A:384-523
1b
d3q6jb3
B:384-523
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
FAD/NAD(P)-binding domain
(331)
Superfamily
:
FAD/NAD(P)-binding domain
(331)
Family
:
FAD/NAD-linked reductases, N-terminal and central domains
(92)
Protein domain
:
NADH-dependent 2-ketopropyl coenzyme M oxidoreductase/carboxylase
(5)
Xanthobacter sp., py2 [TaxId: 35809]
(5)
2a
d3q6ja1
A:2-192,A:314-383
2b
d3q6ja2
A:193-313
2c
d3q6jb1
B:2-192,B:314-383
2d
d3q6jb2
B:193-313
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CATH Domains
(0, 0)
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all CATH domains
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Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_Pyr_redox_3q6jB01 (B:216-299)
1b: PFAM_Pyr_redox_3q6jB02 (B:216-299)
2a: PFAM_Pyr_redox_2_3q6jB03 (B:45-359)
2b: PFAM_Pyr_redox_2_3q6jB04 (B:45-359)
3a: PFAM_Pyr_redox_dim_3q6jB05 (B:387-512)
3b: PFAM_Pyr_redox_dim_3q6jB06 (B:387-512)
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Organisms
(
)
(
)
Clan
:
NADP_Rossmann
(1239)
Family
:
Pyr_redox
(62)
Xanthobacter autotrophicus (strain ATCC BAA-1158 / Py2)
(3)
1a
Pyr_redox-3q6jB01
B:216-299
1b
Pyr_redox-3q6jB02
B:216-299
Family
:
Pyr_redox_2
(69)
Xanthobacter autotrophicus (strain ATCC BAA-1158 / Py2)
(3)
2a
Pyr_redox_2-3q6jB03
B:45-359
2b
Pyr_redox_2-3q6jB04
B:45-359
Clan
:
no clan defined [family: Pyr_redox_dim]
(44)
Family
:
Pyr_redox_dim
(44)
Xanthobacter autotrophicus (strain ATCC BAA-1158 / Py2)
(3)
3a
Pyr_redox_dim-3q6jB05
B:387-512
3b
Pyr_redox_dim-3q6jB06
B:387-512
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