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1LRT
Asym. Unit
Info
Asym.Unit (239 KB)
Biol.Unit 1 (228 KB)
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Title
:
CRYSTAL STRUCTURE OF TERNARY COMPLEX OF TRITRICHOMONAS FOETUS INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE: STRUCTURAL CHARACTERIZATION OF NAD+ SITE IN MICROBIAL ENZYME
Authors
:
L. Gan, G. A. Petsko, L. Hedstrom
Date
:
15 May 02 (Deposition) - 07 Jul 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Ternary Complex, Alpha-Beta Barrel, Flexible Loop, Flap, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. Gan, G. A. Petsko, L. Hedstrom
Crystal Structure Of A Ternary Complex Of Tritrichomonas Foetus Inosine 5'-Monophosphate Dehydrogenase: Nad+ Orients The Active Site Loop For Catalysis
Biochemistry V. 41 13309 2003
(for further references see the
PDB file header
)
[
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Hetero Components
(5, 26)
Info
All Hetero Components
1a: B-OCTYLGLUCOSIDE (BOGa)
1b: B-OCTYLGLUCOSIDE (BOGb)
2a: INOSINIC ACID (IMPa)
2b: INOSINIC ACID (IMPb)
2c: INOSINIC ACID (IMPc)
2d: INOSINIC ACID (IMPd)
3a: POTASSIUM ION (Ka)
3b: POTASSIUM ION (Kb)
3c: POTASSIUM ION (Kc)
3d: POTASSIUM ION (Kd)
4a: BETA-METHYLENE-THIAZOLE-4-CARBOXYA... (TADa)
4b: BETA-METHYLENE-THIAZOLE-4-CARBOXYA... (TADb)
4c: BETA-METHYLENE-THIAZOLE-4-CARBOXYA... (TADc)
4d: BETA-METHYLENE-THIAZOLE-4-CARBOXYA... (TADd)
5a: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSa)
5b: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSb)
5c: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSc)
5d: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSd)
5e: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSe)
5f: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSf)
5g: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSg)
5h: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSh)
5i: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSi)
5j: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSj)
5k: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSk)
5l: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSl)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BOG
2
Ligand/Ion
B-OCTYLGLUCOSIDE
2
IMP
4
Ligand/Ion
INOSINIC ACID
3
K
4
Ligand/Ion
POTASSIUM ION
4
TAD
4
Ligand/Ion
BETA-METHYLENE-THIAZOLE-4-CARBOXYAMIDE-ADENINEDINUCLEOTIDE
5
TRS
12
Ligand/Ion
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
[
close Hetero Component info
]
Sites
(26, 26)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:241 , PHE A:243 , TRP A:269 , BOG A:752 , TAD A:901 , HOH A:994 , ARG C:241 , ASP C:242 , ARG C:244 , GLU C:245 , HOH C:916
BINDING SITE FOR RESIDUE BOG A 751
02
AC2
SOFTWARE
ARG A:241 , ARG A:244 , GLU A:245 , BOG A:751 , HOH A:953 , ARG C:241 , TAD C:903
BINDING SITE FOR RESIDUE BOG A 752
03
AC3
SOFTWARE
GLY A:20 , SER A:22 , ASN A:460 , ASP D:264 , PHE D:266
BINDING SITE FOR RESIDUE K A 1
04
AC4
SOFTWARE
ASP A:264 , PHE A:266 , TRS A:600 , GLY B:20 , SER B:22 , ASN B:460
BINDING SITE FOR RESIDUE K B 1
05
AC5
SOFTWARE
ASP B:264 , PHE B:266 , GLY C:20 , SER C:22 , ASN C:460
BINDING SITE FOR RESIDUE K C 1
06
AC6
SOFTWARE
ASP C:264 , PHE C:266 , GLY D:20 , SER D:22 , ASN D:460
BINDING SITE FOR RESIDUE K D 1
07
AC7
SOFTWARE
ALA A:57 , MET A:59 , GLY A:316 , SER A:317 , CYS A:319 , ASP A:358 , GLY A:359 , GLY A:360 , MET A:379 , LEU A:380 , GLY A:381 , ARG A:382 , TYR A:405 , GLY A:407 , GLU A:408 , GLY A:409 , GLU A:431 , GLY A:432 , TAD A:901 , HOH A:904 , HOH A:922 , HOH A:923 , HOH A:930 , HOH A:1007
BINDING SITE FOR RESIDUE IMP A 801
08
AC8
SOFTWARE
ALA B:57 , MET B:59 , SER B:317 , ILE B:318 , CYS B:319 , ASP B:358 , GLY B:359 , GLY B:360 , GLY B:381 , ARG B:382 , TYR B:405 , GLY B:407 , GLU B:408 , GLY B:409 , TAD B:902 , HOH B:910 , HOH B:915 , HOH B:952 , HOH B:998
BINDING SITE FOR RESIDUE IMP B 802
09
AC9
SOFTWARE
ALA C:57 , MET C:59 , GLY C:316 , SER C:317 , ILE C:318 , CYS C:319 , ASP C:358 , GLY C:359 , GLY C:360 , MET C:379 , GLY C:381 , ARG C:382 , TYR C:405 , GLY C:407 , GLU C:408 , GLY C:409 , TAD C:903 , HOH C:904 , HOH C:928 , HOH C:956 , HOH C:969 , HOH C:1003
BINDING SITE FOR RESIDUE IMP C 803
10
BC1
SOFTWARE
ALA D:57 , MET D:59 , GLY D:316 , SER D:317 , CYS D:319 , ASP D:358 , GLY D:359 , GLY D:360 , MET D:379 , GLY D:381 , ARG D:382 , TYR D:405 , GLY D:407 , GLU D:408 , GLY D:409 , GLU D:431 , GLY D:432 , TAD D:904 , HOH D:910 , HOH D:937 , HOH D:948 , HOH D:980 , HOH D:1002
BINDING SITE FOR RESIDUE IMP D 804
11
BC2
SOFTWARE
THR A:240 , ARG A:241 , ASP A:261 , SER A:262 , SER A:263 , TRP A:269 , GLY A:312 , ILE A:313 , GLY A:314 , GLU A:408 , GLY A:409 , GLU A:431 , TRS A:600 , BOG A:751 , IMP A:801 , HOH A:914 , HOH A:915 , HOH A:922 , HOH A:928 , HOH A:975 , HOH A:976 , HOH A:1025 , HOH A:1048
BINDING SITE FOR RESIDUE TAD A 901
12
BC3
SOFTWARE
THR B:240 , ARG B:241 , ASP B:261 , SER B:262 , SER B:263 , TRP B:269 , GLY B:312 , ILE B:313 , GLY B:314 , GLU B:408 , GLY B:409 , IMP B:802 , HOH B:937 , HOH B:952 , HOH B:958 , HOH B:959 , HOH B:977 , HOH B:980
BINDING SITE FOR RESIDUE TAD B 902
13
BC4
SOFTWARE
ARG A:244 , BOG A:752 , THR C:240 , ARG C:241 , ASP C:261 , SER C:262 , SER C:263 , TRP C:269 , GLY C:312 , ILE C:313 , GLY C:314 , GLU C:408 , GLY C:409 , IMP C:803 , HOH C:905 , HOH C:938 , HOH C:974 , HOH C:975
BINDING SITE FOR RESIDUE TAD C 903
14
BC5
SOFTWARE
THR D:240 , ARG D:241 , ASP D:261 , SER D:262 , SER D:263 , TRP D:269 , GLY D:312 , ILE D:313 , GLY D:314 , ARG D:322 , GLU D:408 , GLY D:409 , GLU D:431 , IMP D:804 , HOH D:920 , HOH D:953 , HOH D:954 , HOH D:986 , HOH D:1002
BINDING SITE FOR RESIDUE TAD D 904
15
BC6
SOFTWARE
SER A:262 , ASP A:264 , SER A:267 , TAD A:901 , HOH A:975 , HOH A:976 , K B:1 , SER B:22 , ASN B:460 , HOH B:969
BINDING SITE FOR RESIDUE TRS A 600
16
BC7
SOFTWARE
LYS A:39 , ALA A:302 , ASP A:303 , GLY A:305 , TYR A:345 , ILE A:351
BINDING SITE FOR RESIDUE TRS A 601
17
BC8
SOFTWARE
ASP C:364 , ARG C:386 , ASN C:446 , ALA C:449 , SER C:450
BINDING SITE FOR RESIDUE TRS C 602
18
BC9
SOFTWARE
ASP B:364 , TYR B:383 , ARG B:386 , ASN B:446 , ALA B:449 , SER B:450
BINDING SITE FOR RESIDUE TRS B 603
19
CC1
SOFTWARE
ASP D:364 , TYR D:383 , ARG D:386 , ASN D:446 , SER D:450
BINDING SITE FOR RESIDUE TRS D 604
20
CC2
SOFTWARE
ALA B:2 , VAL C:339 , ALA C:340 , ASN C:343 , HOH C:911 , HOH C:920 , HOH C:995 , HOH C:1019
BINDING SITE FOR RESIDUE TRS C 605
21
CC3
SOFTWARE
ALA C:2 , HOH C:919 , VAL D:339 , ASN D:343 , HOH D:930 , HOH D:974 , HOH D:984
BINDING SITE FOR RESIDUE TRS D 606
22
CC4
SOFTWARE
VAL A:339 , ALA A:340 , ASN A:343 , HOH A:1008 , HOH A:1009 , HOH A:1039 , ALA D:2 , HOH D:917
BINDING SITE FOR RESIDUE TRS A 607
23
CC5
SOFTWARE
ALA A:2 , HOH A:929 , VAL B:339 , ALA B:340 , ASN B:343 , HOH B:940 , HOH B:942
BINDING SITE FOR RESIDUE TRS B 608
24
CC6
SOFTWARE
TYR D:5 , ASN D:6 , GLU D:7 , ARG D:329 , HOH D:1016
BINDING SITE FOR RESIDUE TRS D 609
25
CC7
SOFTWARE
PRO A:36 , PHE A:40 , GLN A:44 , GLN A:45 , SER A:46 , ASN A:49 , HOH A:961 , LYS B:284
BINDING SITE FOR RESIDUE TRS A 610
26
CC8
SOFTWARE
PHE B:40 , GLN B:44 , GLN B:45 , SER B:46 , ASN B:49 , HOH B:975
BINDING SITE FOR RESIDUE TRS B 611
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
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Sorry, no Info available
[
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: IMP_DH_GMP_RED (A:309-319,B:309-319,C:309-319,D:30...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
IMP_DH_GMP_RED
PS00487
IMP dehydrogenase / GMP reductase signature.
IMDH_TRIFO
309-321
4
A:309-319
B:309-319
C:309-319
D:309-321
[
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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.
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1lrta1 (A:2-100,A:231-485)
1b: SCOP_d1lrtb1 (B:2-100,B:231-485)
1c: SCOP_d1lrtc1 (C:2-100,C:231-485)
1d: SCOP_d1lrtd1 (D:2-100,D:231-485)
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)
(
)
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(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Inosine monophosphate dehydrogenase (IMPDH)
(29)
Family
:
Inosine monophosphate dehydrogenase (IMPDH)
(18)
Protein domain
:
Inosine monophosphate dehydrogenase (IMPDH)
(18)
Tritrichomonas foetus [TaxId: 5724]
(9)
1a
d1lrta1
A:2-100,A:231-485
1b
d1lrtb1
B:2-100,B:231-485
1c
d1lrtc1
C:2-100,C:231-485
1d
d1lrtd1
D:2-100,D:231-485
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1lrtB00 (B:2-485)
1b: CATH_1lrtC00 (C:2-485)
1c: CATH_1lrtA00 (A:2-485)
1d: CATH_1lrtD00 (D:2-485)
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(
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Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Aldolase class I
(887)
Tritrichomonas foetus. Organism_taxid: 5724.
(8)
1a
1lrtB00
B:2-485
1b
1lrtC00
C:2-485
1c
1lrtA00
A:2-485
1d
1lrtD00
D:2-485
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_IMPDH_1lrtD01 (D:8-485)
1b: PFAM_IMPDH_1lrtD02 (D:8-485)
1c: PFAM_IMPDH_1lrtD03 (D:8-485)
1d: PFAM_IMPDH_1lrtD04 (D:8-485)
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Clans
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Organisms
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(
)
Clan
:
TIM_barrel
(694)
Family
:
IMPDH
(16)
Tritrichomonas foetus (Trichomonas foetus)
(7)
1a
IMPDH-1lrtD01
D:8-485
1b
IMPDH-1lrtD02
D:8-485
1c
IMPDH-1lrtD03
D:8-485
1d
IMPDH-1lrtD04
D:8-485
[
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