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3FLK
Asym. Unit
Info
Asym.Unit (261 KB)
Biol.Unit 1 (128 KB)
Biol.Unit 2 (128 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF TARTRATE DEHYDROGENASE FROM PSEUDOMONAS PUTIDA IN COMPLEX WITH NADH, OXALATE AND METAL ION
Authors
:
R. Malik, R. E. Viola
Date
:
18 Dec 08 (Deposition) - 22 Dec 09 (Release) - 30 Oct 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Lyase, Magnesium, Manganese, Nad, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Malik, R. E. Viola
Structural Characterization Of Tartrate Dehydrogenase: A Versatile Enzyme Catalyzing Multiple Reactions.
Acta Crystallogr. , Sect. D V. 66 673 2010
[
close entry info
]
Hetero Components
(7, 73)
Info
All Hetero Components
1a: 2,3-DIHYDROXY-1,4-DITHIOBUTANE (DTTa)
1b: 2,3-DIHYDROXY-1,4-DITHIOBUTANE (DTTb)
1c: 2,3-DIHYDROXY-1,4-DITHIOBUTANE (DTTc)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
3a: SELENOMETHIONINE (MSEa)
3aa: SELENOMETHIONINE (MSEaa)
3ab: SELENOMETHIONINE (MSEab)
3ac: SELENOMETHIONINE (MSEac)
3ad: SELENOMETHIONINE (MSEad)
3ae: SELENOMETHIONINE (MSEae)
3af: SELENOMETHIONINE (MSEaf)
3ag: SELENOMETHIONINE (MSEag)
3ah: SELENOMETHIONINE (MSEah)
3ai: SELENOMETHIONINE (MSEai)
3aj: SELENOMETHIONINE (MSEaj)
3ak: SELENOMETHIONINE (MSEak)
3al: SELENOMETHIONINE (MSEal)
3am: SELENOMETHIONINE (MSEam)
3an: SELENOMETHIONINE (MSEan)
3b: SELENOMETHIONINE (MSEb)
3c: SELENOMETHIONINE (MSEc)
3d: SELENOMETHIONINE (MSEd)
3e: SELENOMETHIONINE (MSEe)
3f: SELENOMETHIONINE (MSEf)
3g: SELENOMETHIONINE (MSEg)
3h: SELENOMETHIONINE (MSEh)
3i: SELENOMETHIONINE (MSEi)
3j: SELENOMETHIONINE (MSEj)
3k: SELENOMETHIONINE (MSEk)
3l: SELENOMETHIONINE (MSEl)
3m: SELENOMETHIONINE (MSEm)
3n: SELENOMETHIONINE (MSEn)
3o: SELENOMETHIONINE (MSEo)
3p: SELENOMETHIONINE (MSEp)
3q: SELENOMETHIONINE (MSEq)
3r: SELENOMETHIONINE (MSEr)
3s: SELENOMETHIONINE (MSEs)
3t: SELENOMETHIONINE (MSEt)
3u: SELENOMETHIONINE (MSEu)
3v: SELENOMETHIONINE (MSEv)
3w: SELENOMETHIONINE (MSEw)
3x: SELENOMETHIONINE (MSEx)
3y: SELENOMETHIONINE (MSEy)
3z: SELENOMETHIONINE (MSEz)
4a: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIa)
4b: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIb)
4c: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIc)
4d: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAId)
5a: AMMONIUM ION (NH4a)
5b: AMMONIUM ION (NH4b)
5c: AMMONIUM ION (NH4c)
5d: AMMONIUM ION (NH4d)
6a: OXALATE ION (OXLa)
6b: OXALATE ION (OXLb)
6c: OXALATE ION (OXLc)
6d: OXALATE ION (OXLd)
7a: SULFATE ION (SO4a)
7b: SULFATE ION (SO4b)
7c: SULFATE ION (SO4c)
7d: SULFATE ION (SO4d)
7e: SULFATE ION (SO4e)
7f: SULFATE ION (SO4f)
7g: SULFATE ION (SO4g)
7h: SULFATE ION (SO4h)
7i: SULFATE ION (SO4i)
7j: SULFATE ION (SO4j)
7k: SULFATE ION (SO4k)
7l: SULFATE ION (SO4l)
7m: SULFATE ION (SO4m)
7n: SULFATE ION (SO4n)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DTT
3
Ligand/Ion
2,3-DIHYDROXY-1,4-DITHIOBUTANE
2
MG
4
Ligand/Ion
MAGNESIUM ION
3
MSE
40
Mod. Amino Acid
SELENOMETHIONINE
4
NAI
4
Ligand/Ion
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
5
NH4
4
Ligand/Ion
AMMONIUM ION
6
OXL
4
Ligand/Ion
OXALATE ION
7
SO4
14
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(33, 33)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:250 , OXL A:403 , HOH A:665 , HOH A:666 , ASP B:225
BINDING SITE FOR RESIDUE MG A 401
02
AC2
SOFTWARE
ILE A:16 , PHE A:75 , ALA A:77 , VAL A:78 , GLY A:79 , PRO A:81 , ASP A:86 , LEU A:94 , ILE A:263 , GLU A:282 , HIS A:285 , GLY A:286 , SER A:287 , ALA A:288 , ILE A:291 , ASN A:298 , OXL A:403 , NH4 A:404 , HOH A:505 , HOH A:517 , HOH A:520 , HOH A:531 , HOH A:548 , HOH A:619 , HOH A:631 , HOH A:667 , HOH A:668 , HOH A:669 , HOH A:671 , ASN B:194 , HIS B:223 , ILE B:226 , ARG B:230
BINDING SITE FOR RESIDUE NAI A 402
03
AC3
SOFTWARE
ARG A:98 , ARG A:108 , ARG A:134 , ASP A:250 , MG A:401 , NAI A:402 , HOH A:600 , LYS B:192 , ASP B:225
BINDING SITE FOR RESIDUE OXL A 403
04
AC4
SOFTWARE
GLY A:76 , GLU A:282 , PRO A:283 , HIS A:285 , NAI A:402
BINDING SITE FOR RESIDUE NH4 A 404
05
AC5
SOFTWARE
ASP A:225 , ASP B:250 , OXL B:402 , HOH B:659 , HOH B:660
BINDING SITE FOR RESIDUE MG A 405
06
AC6
SOFTWARE
ARG A:111 , TRP A:304 , LEU A:308 , HIS A:324 , LEU A:328 , HOH A:721
BINDING SITE FOR RESIDUE SO4 A 406
07
AC7
SOFTWARE
GLN A:234 , ARG A:237 , ARG C:7
BINDING SITE FOR RESIDUE SO4 A 407
08
AC8
SOFTWARE
LYS A:57 , PRO A:60 , ASP A:61 , ASP A:62 , HOH A:693
BINDING SITE FOR RESIDUE SO4 A 408
09
AC9
SOFTWARE
ARG A:182 , GLU A:183 , HOH A:547
BINDING SITE FOR RESIDUE SO4 A 409
10
BC1
SOFTWARE
ASN A:194 , HIS A:223 , ILE A:226 , ARG A:230 , ILE B:16 , ALA B:77 , VAL B:78 , GLY B:79 , PRO B:81 , ASP B:86 , LEU B:94 , ILE B:263 , GLU B:282 , HIS B:285 , GLY B:286 , SER B:287 , ALA B:288 , ASP B:290 , ILE B:291 , ALA B:297 , ASN B:298 , OXL B:402 , NH4 B:403 , HOH B:509 , HOH B:555 , HOH B:562 , HOH B:580 , HOH B:620 , HOH B:661 , HOH B:665 , HOH B:667 , HOH B:669 , HOH B:679
BINDING SITE FOR RESIDUE NAI B 401
11
BC2
SOFTWARE
LYS A:192 , ASP A:225 , MG A:405 , ARG B:98 , ARG B:108 , ARG B:134 , ASP B:250 , NAI B:401 , HOH B:659 , HOH B:662 , HOH B:702
BINDING SITE FOR RESIDUE OXL B 402
12
BC3
SOFTWARE
GLY B:76 , GLU B:282 , PRO B:283 , HIS B:285 , NAI B:401
BINDING SITE FOR RESIDUE NH4 B 403
13
BC4
SOFTWARE
ARG B:111 , TRP B:304 , LEU B:308 , HIS B:324 , LEU B:328 , HOH B:644
BINDING SITE FOR RESIDUE SO4 B 404
14
BC5
SOFTWARE
THR B:152 , GLU B:153 , PRO B:215 , HOH B:673
BINDING SITE FOR RESIDUE SO4 B 405
15
BC6
SOFTWARE
GLN B:234 , ARG B:237 , ARG D:7
BINDING SITE FOR RESIDUE SO4 B 406
16
BC7
SOFTWARE
ARG B:165 , ARG B:206 , HIS B:213 , HOH B:538
BINDING SITE FOR RESIDUE DTT B 407
17
BC8
SOFTWARE
ASP C:250 , ASP C:254 , OXL C:403 , HOH C:521 , HOH C:526 , ASP D:225
BINDING SITE FOR RESIDUE MG C 401
18
BC9
SOFTWARE
ILE C:16 , ALA C:77 , VAL C:78 , GLY C:79 , PRO C:81 , ASP C:86 , LEU C:94 , GLU C:282 , HIS C:285 , GLY C:286 , SER C:287 , ALA C:288 , ASP C:290 , ILE C:291 , ALA C:297 , ASN C:298 , OXL C:403 , NH4 C:404 , HOH C:513 , HOH C:532 , HOH C:551 , HOH C:574 , HOH C:583 , HOH C:588 , HOH C:628 , HOH C:677 , ASN D:194 , HIS D:223 , ILE D:226 , ARG D:230
BINDING SITE FOR RESIDUE NAI C 402
19
CC1
SOFTWARE
ARG C:98 , ARG C:108 , ARG C:134 , ASP C:250 , MG C:401 , NAI C:402 , HOH C:678 , LYS D:192 , ASP D:225
BINDING SITE FOR RESIDUE OXL C 403
20
CC2
SOFTWARE
GLY C:76 , GLU C:282 , PRO C:283 , HIS C:285 , NAI C:402
BINDING SITE FOR RESIDUE NH4 C 404
21
CC3
SOFTWARE
ASP C:225 , ASP D:250 , OXL D:402 , HOH D:705 , HOH D:706
BINDING SITE FOR RESIDUE MG C 405
22
CC4
SOFTWARE
THR C:152 , GLU C:153
BINDING SITE FOR RESIDUE SO4 C 406
23
CC5
SOFTWARE
LYS C:57 , PRO C:60 , ASP C:61
BINDING SITE FOR RESIDUE SO4 C 407
24
CC6
SOFTWARE
ARG C:111 , TRP C:304 , LEU C:308 , HIS C:324 , LEU C:328 , HOH C:652
BINDING SITE FOR RESIDUE SO4 C 408
25
CC7
SOFTWARE
ILE C:226 , LEU C:233 , GLN C:234 , THR D:262 , ILE D:263 , HOH D:685
BINDING SITE FOR RESIDUE DTT C 409
26
CC8
SOFTWARE
ASN C:194 , HIS C:223 , ILE C:226 , ARG C:230 , HOH C:623 , ILE D:16 , ALA D:77 , VAL D:78 , GLY D:79 , PRO D:81 , ASP D:86 , LEU D:94 , ILE D:263 , GLU D:282 , HIS D:285 , GLY D:286 , SER D:287 , ALA D:288 , ASP D:290 , ILE D:291 , ALA D:297 , ASN D:298 , OXL D:402 , NH4 D:403 , HOH D:512 , HOH D:515 , HOH D:534 , HOH D:594 , HOH D:654 , HOH D:707 , HOH D:708
BINDING SITE FOR RESIDUE NAI D 401
27
CC9
SOFTWARE
LYS C:192 , ASP C:225 , MG C:405 , HOH C:535 , ARG D:98 , ARG D:108 , ARG D:134 , ASP D:250 , NAI D:401 , HOH D:764
BINDING SITE FOR RESIDUE OXL D 402
28
DC1
SOFTWARE
GLY D:76 , GLU D:282 , PRO D:283 , HIS D:285 , NAI D:401
BINDING SITE FOR RESIDUE NH4 D 403
29
DC2
SOFTWARE
LYS D:57 , PRO D:60 , ASP D:61 , ASP D:62 , HOH D:671 , HOH D:680
BINDING SITE FOR RESIDUE SO4 D 404
30
DC3
SOFTWARE
ARG D:26 , SER D:358 , HOH D:557 , HOH D:642 , HOH D:675
BINDING SITE FOR RESIDUE SO4 D 405
31
DC4
SOFTWARE
ARG D:111 , TRP D:304 , LEU D:308 , HIS D:324 , LEU D:328 , HOH D:748
BINDING SITE FOR RESIDUE SO4 D 406
32
DC5
SOFTWARE
ARG C:165 , ASN D:151 , HOH D:711
BINDING SITE FOR RESIDUE SO4 D 407
33
DC6
SOFTWARE
ASP D:14 , GLY D:15 , TRP D:80 , PHE D:292 , HOH D:632 , HOH D:668 , HOH D:738
BINDING SITE FOR RESIDUE DTT D 408
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
[
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: IDH_IMDH (A:246-265,B:246-265,C:246-265,D:24...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
IDH_IMDH
PS00470
Isocitrate and isopropylmalate dehydrogenases signature.
TTUC_PSEPU
246-265
4
A:246-265
B:246-265
C:246-265
D:246-265
[
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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_d3flka_ (A:)
1b: SCOP_d3flkb_ (B:)
1c: SCOP_d3flkc_ (C:)
1d: SCOP_d3flkd_ (D:)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Isocitrate/Isopropylmalate dehydrogenase-like
(143)
Superfamily
:
Isocitrate/Isopropylmalate dehydrogenase-like
(143)
Family
:
automated matches
(22)
Protein domain
:
automated matches
(22)
Pseudomonas putida [TaxId: 303]
(2)
1a
d3flka_
A:
1b
d3flkb_
B:
1c
d3flkc_
C:
1d
d3flkd_
D:
[
close SCOP info
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_3flkA00 (A:5-364)
1b: CATH_3flkB00 (B:5-364)
1c: CATH_3flkC00 (C:5-364)
1d: CATH_3flkD00 (D:5-364)
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Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Isopropylmalate Dehydrogenase
(91)
Homologous Superfamily
:
Isopropylmalate Dehydrogenase
(91)
Pseudomonas putida. Organism_taxid: 303. Strain: atcc 17642.
(1)
1a
3flkA00
A:5-364
1b
3flkB00
B:5-364
1c
3flkC00
C:5-364
1d
3flkD00
D:5-364
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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