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1PVN
Asym. Unit
Info
Asym.Unit (253 KB)
Biol.Unit 1 (245 KB)
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(1)
Title
:
THE CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN IMP DEHYDROGENASE CATALYTIC DOMAIN AND A TRANSITION STATE ANALOGUE MZP
Authors
:
L. Gan, M. Seyedsayamdost, S. Shuto, A. Matsuda, G. A. Petsko, L. Hedstrom
Date
:
27 Jun 03 (Deposition) - 22 Jul 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Transition State Analogue, Imp Dehydrogenase, Mizoribine 5'- Monophosphate, Distal Flap, General Base, Drug Selectivity, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. Gan, M. Seyedsayamdost, S. Shuto, A. Matsuda, G. A. Petsko, L. Hedstrom
The Immunosuppressive Agent Mizoribine Monophosphate Forms A Transition State Analogue Complex With Inosine Monophosphate Dehydrogenase
Biochemistry V. 42 857 2003
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 18)
Info
All Hetero Components
1a: POTASSIUM ION (Ka)
1b: POTASSIUM ION (Kb)
1c: POTASSIUM ION (Kc)
1d: POTASSIUM ION (Kd)
1e: POTASSIUM ION (Ke)
1f: POTASSIUM ION (Kf)
1g: POTASSIUM ION (Kg)
1h: POTASSIUM ION (Kh)
2a: 4-CARBAMOYL-1-BETA-D-RIBOFURANOSYL... (MZPa)
2b: 4-CARBAMOYL-1-BETA-D-RIBOFURANOSYL... (MZPb)
2c: 4-CARBAMOYL-1-BETA-D-RIBOFURANOSYL... (MZPc)
2d: 4-CARBAMOYL-1-BETA-D-RIBOFURANOSYL... (MZPd)
3a: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSa)
3b: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSb)
3c: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSc)
3d: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSd)
3e: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSe)
3f: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
K
8
Ligand/Ion
POTASSIUM ION
2
MZP
4
Ligand/Ion
4-CARBAMOYL-1-BETA-D-RIBOFURANOSYL-IMIDAZOLIUM-5-OLATE-5'-PHOSPHATE
3
TRS
6
Ligand/Ion
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
[
close Hetero Component info
]
Sites
(18, 18)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:485 , GLY A:486 , GLY A:487 , GLY D:314 , GLY D:316 , CYS D:319
BINDING SITE FOR RESIDUE K A 981
02
AC2
SOFTWARE
GLY A:314 , GLY A:316 , CYS A:319 , GLU B:485 , GLY B:486 , GLY B:487
BINDING SITE FOR RESIDUE K B 982
03
AC3
SOFTWARE
GLY C:314 , GLY C:316 , CYS C:319 , GLU D:485 , GLY D:486 , GLY D:487
BINDING SITE FOR RESIDUE K D 983
04
AC4
SOFTWARE
ASP C:264 , PHE C:266 , GLY D:20 , SER D:22 , ASN D:460
BINDING SITE FOR RESIDUE K C 984
05
AC5
SOFTWARE
GLY B:314 , GLY B:316 , CYS B:319 , GLU C:485 , GLY C:486 , GLY C:487
BINDING SITE FOR RESIDUE K C 985
06
AC6
SOFTWARE
ASP B:264 , PHE B:266 , GLY C:20 , SER C:22 , ASN C:460
BINDING SITE FOR RESIDUE K B 986
07
AC7
SOFTWARE
ASP A:264 , PHE A:266 , GLY B:20 , SER B:22 , ASN B:460
BINDING SITE FOR RESIDUE K A 987
08
AC8
SOFTWARE
GLY A:20 , SER A:22 , ASN A:460 , ASP D:264 , PHE D:266
BINDING SITE FOR RESIDUE K A 988
09
AC9
SOFTWARE
ALA A:57 , MET A:59 , GLY A:316 , SER A:317 , ILE A:318 , 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 , ARG A:418 , TYR A:419 , GLU A:431 , GLY A:432 , HOH A:1004 , HOH A:1010 , HOH A:1012 , HOH A:1028 , HOH A:1029 , HOH A:1053
BINDING SITE FOR RESIDUE MZP A 971
10
BC1
SOFTWARE
ALA B:57 , MET B:59 , GLY B:316 , SER B:317 , ILE B:318 , CYS B:319 , ASP B:358 , GLY B:359 , GLY B:360 , MET B:379 , LEU B:380 , GLY B:381 , ARG B:382 , TYR B:405 , GLY B:407 , GLU B:408 , GLY B:409 , ARG B:418 , TYR B:419 , GLU B:431 , GLY B:432 , HOH B:997 , HOH B:1000 , HOH B:1008 , HOH B:1023 , HOH B:1036 , HOH B:1041 , HOH B:1046 , HOH B:1124
BINDING SITE FOR RESIDUE MZP B 972
11
BC2
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 , LEU C:380 , GLY C:381 , ARG C:382 , TYR C:405 , GLY C:407 , GLU C:408 , GLY C:409 , ARG C:418 , TYR C:419 , GLU C:431 , GLY C:432 , HOH C:998 , HOH C:1005 , HOH C:1007 , HOH C:1014 , HOH C:1015 , HOH C:1039
BINDING SITE FOR RESIDUE MZP C 973
12
BC3
SOFTWARE
ALA D:57 , MET D:59 , GLY D:316 , SER D:317 , ILE D:318 , CYS D:319 , ASP D:358 , GLY D:359 , GLY D:360 , MET D:379 , LEU D:380 , GLY D:381 , ARG D:382 , TYR D:405 , GLY D:407 , GLU D:408 , GLY D:409 , ARG D:418 , TYR D:419 , GLU D:431 , GLY D:432 , HOH D:1001 , HOH D:1005 , HOH D:1017 , HOH D:1022 , HOH D:1037 , HOH D:1051
BINDING SITE FOR RESIDUE MZP D 974
13
BC4
SOFTWARE
ASP B:364 , TYR B:383 , ARG B:386 , ASN B:446 , ALA B:449 , SER B:450 , LYS B:453 , HOH B:1192
BINDING SITE FOR RESIDUE TRS B 991
14
BC5
SOFTWARE
ALA B:2 , VAL C:339 , ASN C:343 , HOH C:997 , HOH C:999 , HOH C:1051 , HOH C:1063
BINDING SITE FOR RESIDUE TRS C 992
15
BC6
SOFTWARE
VAL A:339 , ALA A:340 , ASN A:343 , HOH A:1001 , HOH A:1018 , HOH A:1040 , HOH A:1093 , HOH A:1097 , ALA D:2
BINDING SITE FOR RESIDUE TRS A 993
16
BC7
SOFTWARE
ALA A:2 , HOH A:1008 , VAL B:339 , ASN B:343 , HOH B:999 , HOH B:1075 , HOH B:1077 , HOH B:1176 , HOH B:1233
BINDING SITE FOR RESIDUE TRS B 994
17
BC8
SOFTWARE
ALA C:2 , HOH C:1040 , VAL D:339 , ASN D:343 , HOH D:998 , HOH D:1011 , HOH D:1085
BINDING SITE FOR RESIDUE TRS D 995
18
BC9
SOFTWARE
TYR A:15 , ILE A:336 , LEU A:477 , HOH A:1062 , HOH D:999 , HOH D:1069 , HOH D:1084
BINDING SITE FOR RESIDUE TRS A 996
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: IMP_DH_GMP_RED (A:309-321,B:309-321,C:309-321,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:309-321
B:309-321
C:309-321
D:309-321
[
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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_d1pvna1 (A:2-99,A:231-494)
1b: SCOP_d1pvnb1 (B:2-99,B:231-494)
1c: SCOP_d1pvnc1 (C:2-99,C:231-494)
1d: SCOP_d1pvnd1 (D:2-99,D:231-494)
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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
d1pvna1
A:2-99,A:231-494
1b
d1pvnb1
B:2-99,B:231-494
1c
d1pvnc1
C:2-99,C:231-494
1d
d1pvnd1
D:2-99,D:231-494
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1pvnA00 (A:2-494)
1b: CATH_1pvnB00 (B:2-494)
1c: CATH_1pvnC00 (C:2-494)
1d: CATH_1pvnD00 (D:2-494)
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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
1pvnA00
A:2-494
1b
1pvnB00
B:2-494
1c
1pvnC00
C:2-494
1d
1pvnD00
D:2-494
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_IMPDH_1pvnD01 (D:8-489)
1b: PFAM_IMPDH_1pvnD02 (D:8-489)
1c: PFAM_IMPDH_1pvnD03 (D:8-489)
1d: PFAM_IMPDH_1pvnD04 (D:8-489)
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(
)
Clan
:
TIM_barrel
(694)
Family
:
IMPDH
(16)
Tritrichomonas foetus (Trichomonas foetus)
(7)
1a
IMPDH-1pvnD01
D:8-489
1b
IMPDH-1pvnD02
D:8-489
1c
IMPDH-1pvnD03
D:8-489
1d
IMPDH-1pvnD04
D:8-489
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Asym.Unit (253 KB)
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