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2O2Q
Biol. Unit 1
Info
Asym.Unit (367 KB)
Biol.Unit 1 (358 KB)
Biol.Unit 2 (709 KB)
Biol.Unit 3 (707 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF RAT 10'FORMYLTETRAHYDROFOLATE DEHYDROGENASE IN COMPLEX WITH NADP
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
:
2.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: A,B,C,D (2x)
Biol. Unit 3: 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, 36)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
3a: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPa)
3b: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPb)
3c: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPc)
3d: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPd)
4a: SULFATE ION (SO4a)
4aa: SULFATE ION (SO4aa)
4ab: SULFATE ION (SO4ab)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
4e: SULFATE ION (SO4e)
4f: SULFATE ION (SO4f)
4g: SULFATE ION (SO4g)
4h: SULFATE ION (SO4h)
4i: SULFATE ION (SO4i)
4j: SULFATE ION (SO4j)
4k: SULFATE ION (SO4k)
4l: SULFATE ION (SO4l)
4m: SULFATE ION (SO4m)
4n: SULFATE ION (SO4n)
4o: SULFATE ION (SO4o)
4p: SULFATE ION (SO4p)
4q: SULFATE ION (SO4q)
4r: SULFATE ION (SO4r)
4s: SULFATE ION (SO4s)
4t: SULFATE ION (SO4t)
4u: SULFATE ION (SO4u)
4v: SULFATE ION (SO4v)
4w: SULFATE ION (SO4w)
4x: SULFATE ION (SO4x)
4y: SULFATE ION (SO4y)
4z: SULFATE ION (SO4z)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
4
Ligand/Ion
GLYCEROL
2
MG
-1
Ligand/Ion
MAGNESIUM ION
3
NAP
4
Ligand/Ion
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
4
SO4
28
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(40, 40)
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)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
NAP A:903
BINDING SITE FOR RESIDUE MG A 2001
02
AC2
SOFTWARE
NAP B:903
BINDING SITE FOR RESIDUE MG B 2002
03
AC3
SOFTWARE
NAP C:903
BINDING SITE FOR RESIDUE MG C 2003
04
AC4
SOFTWARE
NAP D:903
BINDING SITE FOR RESIDUE MG D 2004
05
AC5
SOFTWARE
LYS A:852 , ARG C:554
BINDING SITE FOR RESIDUE SO4 A 3001
06
AC6
SOFTWARE
ARG A:554 , LYS C:852 , HOH C:3110
BINDING SITE FOR RESIDUE SO4 A 3002
07
AC7
SOFTWARE
ARG B:554 , ASP D:851 , LYS D:852 , HOH D:3205
BINDING SITE FOR RESIDUE SO4 D 3003
08
AC8
SOFTWARE
LYS B:852 , HOH B:3146 , ARG D:554
BINDING SITE FOR RESIDUE SO4 B 3004
09
AC9
SOFTWARE
ARG B:636 , PRO B:641 , HOH B:3322
BINDING SITE FOR RESIDUE SO4 B 3005
10
BC1
SOFTWARE
ARG A:636 , PRO A:641 , HOH A:3470 , HOH A:3473
BINDING SITE FOR RESIDUE SO4 A 3006
11
BC2
SOFTWARE
ARG C:636 , PRO C:641
BINDING SITE FOR RESIDUE SO4 C 3007
12
BC3
SOFTWARE
ARG D:636 , PRO D:641
BINDING SITE FOR RESIDUE SO4 D 3008
13
BC4
SOFTWARE
ARG B:764
BINDING SITE FOR RESIDUE SO4 B 3009
14
BC5
SOFTWARE
ARG C:764
BINDING SITE FOR RESIDUE SO4 C 3010
15
BC6
SOFTWARE
ARG A:764 , TYR A:799
BINDING SITE FOR RESIDUE SO4 A 3011
16
BC7
SOFTWARE
ARG D:764
BINDING SITE FOR RESIDUE SO4 D 3012
17
BC8
SOFTWARE
LYS C:669 , ARG C:894 , ILE C:895 , HOH C:3035 , HOH C:3105 , HOH C:3170 , HOH C:3183 , HOH C:3402 , GLY D:881 , LYS D:882
BINDING SITE FOR RESIDUE SO4 C 3013
18
BC9
SOFTWARE
GLY A:881 , LYS A:882 , HOH A:3028 , HOH A:3249 , LYS B:669 , LEU B:893 , ARG B:894 , ILE B:895 , HOH B:3065
BINDING SITE FOR RESIDUE SO4 A 3014
19
CC1
SOFTWARE
LYS A:669 , LEU A:893 , ARG A:894 , ILE A:895 , HOH A:3173 , HOH A:3203 , HOH A:3363 , GLY B:881 , LYS B:882 , HOH B:3027
BINDING SITE FOR RESIDUE SO4 A 3015
20
CC2
SOFTWARE
GLY C:881 , LYS C:882 , LYS D:669 , LEU D:893 , ARG D:894 , ILE D:895 , HOH D:3030 , HOH D:3120 , HOH D:3208 , HOH D:3282
BINDING SITE FOR RESIDUE SO4 D 3016
21
CC3
SOFTWARE
TYR A:848 , ARG C:551 , ARG C:554
BINDING SITE FOR RESIDUE SO4 C 3017
22
CC4
SOFTWARE
ARG A:551 , ARG A:554 , TYR C:848 , LYS C:852
BINDING SITE FOR RESIDUE SO4 A 3018
23
CC5
SOFTWARE
ARG B:551 , ARG B:554 , TYR D:848
BINDING SITE FOR RESIDUE SO4 B 3019
24
CC6
SOFTWARE
TYR B:848 , ARG D:551 , ARG D:554
BINDING SITE FOR RESIDUE SO4 D 3020
25
CC7
SOFTWARE
ASN A:548 , HOH A:3165 , HOH A:3315 , HOH A:3466 , GLN B:528
BINDING SITE FOR RESIDUE SO4 A 3021
26
CC8
SOFTWARE
GLN A:528 , ASN B:548 , HOH B:3190 , HOH B:3328 , HOH B:3361
BINDING SITE FOR RESIDUE SO4 B 3022
27
CC9
SOFTWARE
ASN C:548 , HOH C:3252 , HOH C:3294 , HOH C:3491 , LYS D:520 , GLN D:528
BINDING SITE FOR RESIDUE SO4 C 3023
28
DC1
SOFTWARE
ASN A:738 , GLU A:741 , ARG A:781 , HOH A:3201 , HOH A:3476 , HOH C:3297
BINDING SITE FOR RESIDUE SO4 A 3024
29
DC2
SOFTWARE
THR B:445 , ASN B:738 , GLU B:741 , ARG B:781 , HOH B:3158
BINDING SITE FOR RESIDUE SO4 B 3025
30
DC3
SOFTWARE
ASN C:738 , ARG C:781 , HOH C:3068
BINDING SITE FOR RESIDUE SO4 C 3026
31
DC4
SOFTWARE
ASN D:738 , ARG D:781 , HOH D:3393 , HOH D:3488
BINDING SITE FOR RESIDUE SO4 D 3027
32
DC5
SOFTWARE
LEU A:416 , THR A:417 , LYS C:415 , ARG C:742
BINDING SITE FOR RESIDUE SO4 C 3028
33
DC6
SOFTWARE
VAL A:570 , ILE A:571 , TRP A:573 , ASN A:574 , 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 , GLY A:650 , SER A:651 , VAL A:654 , HIS A:657 , ILE A:658 , GLU A:673 , LEU A:674 , GLY A:675 , CYS A:707 , GLU A:804 , PHE A:806 , LEU A:834 , PHE A:872 , MG A:2001 , HOH A:3128 , HOH A:3139 , HOH A:3148 , HOH A:3149 , HOH A:3199 , HOH A:3200 , HOH A:3288 , HOH A:3322 , HOH A:3325 , HOH A:3364
BINDING SITE FOR RESIDUE NAP A 903
34
DC7
SOFTWARE
VAL B:570 , ILE B:571 , TRP B:573 , ASN B:574 , 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 , GLU B:673 , LEU B:674 , GLY B:675 , CYS B:707 , GLU B:804 , PHE B:806 , LEU B:834 , PHE B:872 , MG B:2002 , HOH B:3066 , HOH B:3085 , HOH B:3160 , HOH B:3166 , HOH B:3198 , HOH B:3204 , HOH B:3337 , HOH B:3339
BINDING SITE FOR RESIDUE NAP B 903
35
DC8
SOFTWARE
VAL C:570 , ILE C:571 , TRP C:573 , ASN C:574 , 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 , GLY C:650 , SER C:651 , VAL C:654 , HIS C:657 , ILE C:658 , GLU C:673 , LEU C:674 , GLY C:675 , CYS C:707 , GLU C:804 , PHE C:806 , LEU C:834 , PHE C:872 , MG C:2003 , HOH C:3087 , HOH C:3097 , HOH C:3122 , HOH C:3126 , HOH C:3165 , HOH C:3230 , HOH C:3376 , HOH C:3393 , HOH C:3407 , HOH C:3483
BINDING SITE FOR RESIDUE NAP C 903
36
DC9
SOFTWARE
VAL D:570 , ILE D:571 , TRP D:573 , ASN D:574 , LYS D:597 , ALA D:599 , GLN D:600 , SER D:629 , GLY D:630 , GLY D:634 , GLN D:635 , PHE D:648 , THR D:649 , GLY D:650 , SER D:651 , VAL D:654 , HIS D:657 , ILE D:658 , GLU D:673 , LEU D:674 , GLY D:675 , CYS D:707 , GLU D:804 , PHE D:806 , LEU D:834 , PHE D:872 , MG D:2004 , HOH D:3062 , HOH D:3076 , HOH D:3114 , HOH D:3164 , HOH D:3170 , HOH D:3229 , HOH D:3295 , HOH D:3358 , HOH D:3368
BINDING SITE FOR RESIDUE NAP D 903
37
EC1
SOFTWARE
TYR A:575 , TRP A:582 , ASN A:706 , ILE A:708 , THR A:866
BINDING SITE FOR RESIDUE GOL A 1
38
EC2
SOFTWARE
TYR B:575 , MET B:578 , PHE B:701 , ASN B:706 , ASN B:864 , THR B:866
BINDING SITE FOR RESIDUE GOL B 2
39
EC3
SOFTWARE
TYR C:575 , TRP C:582 , PHE C:701 , ASN C:706 , ASN C:864 , THR C:866 , HOH C:3447
BINDING SITE FOR RESIDUE GOL C 3
40
EC4
SOFTWARE
TYR D:575 , MET D:578 , PHE D:701 , ASN D:706 , ASN D:864 , THR D:866
BINDING SITE FOR RESIDUE GOL D 4
[
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
(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...)
;
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d2o2qa_ (A:)
1b: SCOP_d2o2qb_ (B:)
1c: SCOP_d2o2qc_ (C:)
1d: SCOP_d2o2qd_ (D:)
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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
d2o2qa_
A:
1b
d2o2qb_
B:
1c
d2o2qc_
C:
1d
d2o2qd_
D:
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_2o2qA01 (A:410-675,A:868-902)
1b: CATH_2o2qC01 (C:410-675,C:868-902)
1c: CATH_2o2qD01 (D:410-675,D:868-902)
1d: CATH_2o2qB01 (B:410-675,B:868-902)
2a: CATH_2o2qA02 (A:676-867)
2b: CATH_2o2qC02 (C:676-867)
2c: CATH_2o2qD02 (D:676-867)
2d: CATH_2o2qB02 (B:676-867)
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Architectures
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Topologies
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Homologous Superfamilies
(
)
(
)
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
2o2qA01
A:410-675,A:868-902
1b
2o2qC01
C:410-675,C:868-902
1c
2o2qD01
D:410-675,D:868-902
1d
2o2qB01
B:410-675,B: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
2o2qA02
A:676-867
2b
2o2qC02
C:676-867
2c
2o2qD02
D:676-867
2d
2o2qB02
B:676-867
[
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Pfam Domains
(0, 0)
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all PFAM domains
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