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Asym. Unit
Info
Asym.Unit (342 KB)
Biol.Unit 1 (334 KB)
Biol.Unit 2 (662 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF RAT 10'FORMYLTETRAHYDROFOLATE DEHYDROGENASE IN COMPLEX WITH NADPH
Authors
:
Y. Tsybovsky, H. Donato, N. I. Krupenko, C. Davies, S. A. Krupenko
Date
:
30 Nov 06 (Deposition) - 06 Mar 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: A,B,C,D (2x)
Keywords
:
Aldehyde Dehydrogenase, Fdh, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Tsybovsky, H. Donato, N. I. Krupenko, C. Davies, S. A. Krupenko
Crystal Structures Of The Carboxyl Terminal Domain Of Rat 10-Formyltetrahydrofolate Dehydrogenase: Implications For The Catalytic Mechanism Of Aldehyde Dehydrogenases.
Biochemistry V. 46 2917 2007
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Hetero Components
(3, 29)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
2a: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPa)
2b: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPb)
2c: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPc)
2d: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPd)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
3f: SULFATE ION (SO4f)
3g: SULFATE ION (SO4g)
3h: SULFATE ION (SO4h)
3i: SULFATE ION (SO4i)
3j: SULFATE ION (SO4j)
3k: SULFATE ION (SO4k)
3l: SULFATE ION (SO4l)
3m: SULFATE ION (SO4m)
3n: SULFATE ION (SO4n)
3o: SULFATE ION (SO4o)
3p: SULFATE ION (SO4p)
3q: SULFATE ION (SO4q)
3r: SULFATE ION (SO4r)
3s: SULFATE ION (SO4s)
3t: SULFATE ION (SO4t)
3u: SULFATE ION (SO4u)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
4
Ligand/Ion
GLYCEROL
2
NDP
4
Ligand/Ion
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
3
SO4
21
Ligand/Ion
SULFATE ION
[
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Sites
(29, 29)
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)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LYS A:852 , ARG C:554 , HOH C:3216
BINDING SITE FOR RESIDUE SO4 C 2001
02
AC2
SOFTWARE
ARG A:554 , HOH A:3029 , LYS C:852
BINDING SITE FOR RESIDUE SO4 A 2002
03
AC3
SOFTWARE
ARG B:554 , LYS D:852 , HOH D:3123
BINDING SITE FOR RESIDUE SO4 B 2003
04
AC4
SOFTWARE
LYS B:852 , ARG D:554 , HOH D:3036
BINDING SITE FOR RESIDUE SO4 D 2004
05
AC5
SOFTWARE
ARG B:636 , PRO B:641 , HOH B:3174
BINDING SITE FOR RESIDUE SO4 B 2005
06
AC6
SOFTWARE
ARG A:636
BINDING SITE FOR RESIDUE SO4 A 2006
07
AC7
SOFTWARE
ARG C:636 , PRO C:641
BINDING SITE FOR RESIDUE SO4 C 2007
08
AC8
SOFTWARE
ARG D:636 , PRO D:641
BINDING SITE FOR RESIDUE SO4 D 2008
09
AC9
SOFTWARE
ARG B:764 , TYR B:799
BINDING SITE FOR RESIDUE SO4 B 2009
10
BC1
SOFTWARE
ARG C:764
BINDING SITE FOR RESIDUE SO4 C 2010
11
BC2
SOFTWARE
ARG A:764
BINDING SITE FOR RESIDUE SO4 A 2011
12
BC3
SOFTWARE
ARG D:764
BINDING SITE FOR RESIDUE SO4 D 2012
13
BC4
SOFTWARE
LYS C:669 , LEU C:893 , ARG C:894 , ILE C:895 , HOH C:3192 , GLY D:881 , LYS D:882 , HOH D:3066
BINDING SITE FOR RESIDUE SO4 C 2013
14
BC5
SOFTWARE
GLY A:881 , LYS A:882 , LYS B:669 , LEU B:893 , ARG B:894 , ILE B:895 , HOH B:3004 , HOH B:3175
BINDING SITE FOR RESIDUE SO4 B 2014
15
BC6
SOFTWARE
LYS A:669 , LEU A:893 , ARG A:894 , ILE A:895 , HOH A:3159 , HOH A:3174 , GLY B:881 , LYS B:882 , HOH B:3019
BINDING SITE FOR RESIDUE SO4 A 2015
16
BC7
SOFTWARE
GLY C:881 , LYS C:882 , LYS D:669 , LEU D:893 , ARG D:894 , ILE D:895 , HOH D:3007 , HOH D:3160 , HOH D:3214
BINDING SITE FOR RESIDUE SO4 D 2016
17
BC8
SOFTWARE
LEU A:416 , THR A:417 , LYS C:415 , ARG C:742
BINDING SITE FOR RESIDUE SO4 C 2017
18
BC9
SOFTWARE
TYR A:848 , ARG C:551 , ARG C:554
BINDING SITE FOR RESIDUE SO4 C 2018
19
CC1
SOFTWARE
ARG A:551 , ARG A:554 , TYR C:848
BINDING SITE FOR RESIDUE SO4 A 2019
20
CC2
SOFTWARE
ARG B:551 , ARG B:554 , TYR D:848
BINDING SITE FOR RESIDUE SO4 B 2020
21
CC3
SOFTWARE
TYR B:848 , ARG D:551 , ARG D:554
BINDING SITE FOR RESIDUE SO4 D 2021
22
CC4
SOFTWARE
VAL A:570 , ILE A:571 , TRP A:573 , LYS A:597 , ALA A:599 , GLN A:600 , SER A:629 , GLY A:630 , GLY A:634 , GLN A:635 , PHE A:648 , THR A:649 , SER A:651 , VAL A:654 , HIS A:657 , ILE A:658 , HOH A:3027 , HOH A:3046 , HOH A:3047 , HOH A:3074 , HOH A:3109
BINDING SITE FOR RESIDUE NDP A 903
23
CC5
SOFTWARE
VAL B:570 , ILE B:571 , TRP B:573 , LYS B:597 , ALA B:599 , GLN B:600 , SER B:629 , GLY B:630 , GLY B:634 , GLN B:635 , PHE B:648 , THR B:649 , GLY B:650 , SER B:651 , VAL B:654 , HIS B:657 , ILE B:658 , HOH B:3023 , HOH B:3083 , HOH B:3110 , HOH B:3137 , HOH B:3144
BINDING SITE FOR RESIDUE NDP B 903
24
CC6
SOFTWARE
VAL C:570 , ILE C:571 , TRP C:573 , LYS C:597 , ALA C:599 , GLN C:600 , SER C:629 , GLY C:630 , GLY C:634 , GLN C:635 , PHE C:648 , THR C:649 , SER C:651 , VAL C:654 , HIS C:657 , ILE C:658 , HOH C:3043 , HOH C:3044 , HOH C:3053 , HOH C:3058 , HOH C:3139
BINDING SITE FOR RESIDUE NDP C 903
25
CC7
SOFTWARE
VAL D:570 , ILE D:571 , TRP D:573 , LYS D:597 , ALA D:599 , GLN D:600 , SER D:629 , GLY D:630 , GLY D:634 , GLN D:635 , PHE D:648 , SER D:651 , VAL D:654 , HIS D:657 , ILE D:658 , HOH D:3030 , HOH D:3042 , HOH D:3062 , HOH D:3081 , HOH D:3146 , HOH D:3180
BINDING SITE FOR RESIDUE NDP D 903
26
CC8
SOFTWARE
TYR A:575 , MET A:578 , ASN A:706 , CYS A:707 , ILE A:708 , THR A:866
BINDING SITE FOR RESIDUE GOL A 3001
27
CC9
SOFTWARE
MET B:578 , ASN B:706 , ASN B:864 , THR B:866
BINDING SITE FOR RESIDUE GOL B 3002
28
DC1
SOFTWARE
TYR C:575 , MET C:578 , ASN C:706 , ASN C:864 , THR C:866
BINDING SITE FOR RESIDUE GOL C 3003
29
DC2
SOFTWARE
TYR D:575 , MET D:578 , ASN D:706 , ASN D:864 , THR D:866
BINDING SITE FOR RESIDUE GOL D 3004
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: ALDEHYDE_DEHYDR_GLU (A:672-679,B:672-679,C:672-679,D:67...)
2: ALDEHYDE_DEHYDR_CYS (A:700-711,B:700-711,C:700-711,D:70...)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ALDEHYDE_DEHYDR_GLU
PS00687
Aldehyde dehydrogenases glutamic acid active site.
AL1L1_RAT
672-679
4
A:672-679
B:672-679
C:672-679
D:672-679
2
ALDEHYDE_DEHYDR_CYS
PS00070
Aldehyde dehydrogenases cysteine active site.
AL1L1_RAT
700-711
4
A:700-711
B:700-711
C:700-711
D:700-711
[
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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
(1, 4)
Info
All SCOP Domains
1a: SCOP_d2o2ra_ (A:)
1b: SCOP_d2o2rb_ (B:)
1c: SCOP_d2o2rc_ (C:)
1d: SCOP_d2o2rd_ (D:)
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Classes
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(
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
ALDH-like
(168)
Superfamily
:
ALDH-like
(168)
Family
:
automated matches
(88)
Protein domain
:
automated matches
(88)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(12)
1a
d2o2ra_
A:
1b
d2o2rb_
B:
1c
d2o2rc_
C:
1d
d2o2rd_
D:
[
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_2o2rA01 (A:410-675,A:868-902)
1b: CATH_2o2rB01 (B:410-675,B:868-902)
1c: CATH_2o2rC01 (C:410-675,C:868-902)
1d: CATH_2o2rD01 (D:410-675,D:868-902)
2a: CATH_2o2rA02 (A:676-867)
2b: CATH_2o2rB02 (B:676-867)
2c: CATH_2o2rC02 (C:676-867)
2d: CATH_2o2rD02 (D:676-867)
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Aldehyde Dehydrogenase; Chain A, domain 1
(86)
Homologous Superfamily
:
Aldehyde Dehydrogenase; Chain A, domain 1
(86)
Norway rat (Rattus norvegicus)
(5)
1a
2o2rA01
A:410-675,A:868-902
1b
2o2rB01
B:410-675,B:868-902
1c
2o2rC01
C:410-675,C:868-902
1d
2o2rD01
D:410-675,D:868-902
Topology
:
Aldehyde Dehydrogenase; Chain A, domain 2
(89)
Homologous Superfamily
:
Aldehyde Dehydrogenase; Chain A, domain 2
(89)
Norway rat (Rattus norvegicus)
(5)
2a
2o2rA02
A:676-867
2b
2o2rB02
B:676-867
2c
2o2rC02
C:676-867
2d
2o2rD02
D:676-867
[
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]
Pfam Domains
(0, 0)
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all PFAM domains
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