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1R2R
Biol. Unit 1
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Asym.Unit (185 KB)
Biol.Unit 1 (90 KB)
Biol.Unit 2 (91 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF RABBIT MUSCLE TRIOSEPHOSPHATE ISOMERASE
Authors
:
R. Aparicio, S. T. Ferreira, I. Polikarpov
Date
:
29 Sep 03 (Deposition) - 23 Dec 03 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.50
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Tim; Closed Loop Conformation In The Ligand-Free State; Conformational Heterogeneity; Tim-Barrel, Isomerase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Aparicio, S. T. Ferreira, I. Polikarpov
Closed Conformation Of The Active Site Loop Of Rabbit Muscl Triosephosphate Isomerase In The Absence Of Substrate: Evidence Of Conformational Heterogeneity.
J. Mol. Biol. V. 334 1023 2003
(for further references see the
PDB file header
)
[
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Hetero Components
(1, 8)
Info
All Hetero Components
1a: DIMETHYL SULFOXIDE (DMSa)
1b: DIMETHYL SULFOXIDE (DMSb)
1c: DIMETHYL SULFOXIDE (DMSc)
1d: DIMETHYL SULFOXIDE (DMSd)
1e: DIMETHYL SULFOXIDE (DMSe)
1f: DIMETHYL SULFOXIDE (DMSf)
1g: DIMETHYL SULFOXIDE (DMSg)
1h: DIMETHYL SULFOXIDE (DMSh)
1i: DIMETHYL SULFOXIDE (DMSi)
1j: DIMETHYL SULFOXIDE (DMSj)
1k: DIMETHYL SULFOXIDE (DMSk)
1l: DIMETHYL SULFOXIDE (DMSl)
1m: DIMETHYL SULFOXIDE (DMSm)
1n: DIMETHYL SULFOXIDE (DMSn)
1o: DIMETHYL SULFOXIDE (DMSo)
1p: DIMETHYL SULFOXIDE (DMSp)
1q: DIMETHYL SULFOXIDE (DMSq)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
2e: MAGNESIUM ION (MGe)
2f: MAGNESIUM ION (MGf)
2g: MAGNESIUM ION (MGg)
2h: MAGNESIUM ION (MGh)
2i: MAGNESIUM ION (MGi)
3a: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSa)
3b: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DMS
8
Ligand/Ion
DIMETHYL SULFOXIDE
2
MG
-1
Ligand/Ion
MAGNESIUM ION
3
TRS
-1
Ligand/Ion
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
[
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]
Sites
(13, 13)
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: BC8 (SOFTWARE)
12: CC1 (SOFTWARE)
13: CC4 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR A:89 , TRP A:90 , GLY A:122
BINDING SITE FOR RESIDUE DMS A 249
02
AC2
SOFTWARE
LYS A:218 , SER A:222 , ALA A:246 , LYS A:247
BINDING SITE FOR RESIDUE DMS A 253
03
AC3
SOFTWARE
LYS A:68 , HOH A:311 , HOH A:545 , GLU D:135 , ALA D:136
BINDING SITE FOR RESIDUE DMS A 255
04
AC4
SOFTWARE
ARG B:99 , ASP B:106 , GLN B:146 , HOH B:538 , HOH B:822
BINDING SITE FOR RESIDUE MG B 257
05
AC5
SOFTWARE
THR B:89 , TRP B:90 , GLY B:120 , GLY B:122 , LYS B:159
BINDING SITE FOR RESIDUE DMS B 249
06
AC6
SOFTWARE
ASN B:20
BINDING SITE FOR RESIDUE DMS B 250
07
AC7
SOFTWARE
ARG B:134 , GLU B:183 , LYS B:187
BINDING SITE FOR RESIDUE DMS B 252
08
AC8
SOFTWARE
GLY A:103 , LEU A:108 , HOH A:515 , HOH A:543 , VAL B:101 , LYS D:141
BINDING SITE FOR RESIDUE DMS B 255
09
AC9
SOFTWARE
SER B:197 , ASP B:198 , HOH B:613
BINDING SITE FOR RESIDUE DMS B 256
10
BC1
SOFTWARE
HOH B:838 , HOH B:840 , HOH B:1156 , HOH C:832 , HOH C:834 , HOH C:836
BINDING SITE FOR RESIDUE MG B 261
11
BC8
SOFTWARE
SER A:194 , HOH A:492 , GLU B:186 , ASP C:132
BINDING SITE FOR RESIDUE DMS C 254
12
CC1
SOFTWARE
ALA B:136 , HOH C:975 , HOH C:1104 , HOH C:1114 , VAL D:101 , PHE D:102
BINDING SITE FOR RESIDUE DMS D 254
13
CC4
SOFTWARE
HOH B:835 , HOH B:1160 , HOH B:1166 , HOH D:850 , HOH D:1158 , HOH D:1162 , HOH D:1164
BINDING SITE FOR RESIDUE MG D 249
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: TIM_2 (A:5-246,B:5-246)
2: TIM_1 (A:163-173,B:163-173)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TIM_2
PS51440
Triosephosphate isomerase (TIM) family profile.
TPIS_RABIT
5-246
2
A:5-246
B:5-246
-
-
2
TIM_1
PS00171
Triosephosphate isomerase active site.
TPIS_RABIT
163-173
2
A:163-173
B:163-173
-
-
[
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1r2ra_ (A:)
1b: SCOP_d1r2rb_ (B:)
1c: SCOP_d1r2rc_ (C:)
1d: SCOP_d1r2rd_ (D:)
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Triosephosphate isomerase (TIM)
(148)
Family
:
Triosephosphate isomerase (TIM)
(128)
Protein domain
:
Triosephosphate isomerase
(126)
Rabbit (Oryctolagus cuniculus) [TaxId: 9986]
(4)
1a
d1r2ra_
A:
1b
d1r2rb_
B:
1c
d1r2rc_
C:
1d
d1r2rd_
D:
[
close SCOP info
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1r2rB00 (B:2-248)
1b: CATH_1r2rC00 (C:2-248)
1c: CATH_1r2rD00 (D:2-248)
1d: CATH_1r2rA00 (A:3-248)
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Topologies
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)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Aldolase class I
(887)
Rabbit (Oryctolagus cuniculus)
(27)
1a
1r2rB00
B:2-248
1b
1r2rC00
C:2-248
1c
1r2rD00
D:2-248
1d
1r2rA00
A:3-248
[
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_TIM_1r2rD01 (D:6-244)
1b: PFAM_TIM_1r2rD02 (D:6-244)
1c: PFAM_TIM_1r2rD03 (D:6-244)
1d: PFAM_TIM_1r2rD04 (D:6-244)
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Clans
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Organisms
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)
(
)
Clan
:
TIM_barrel
(694)
Family
:
TIM
(80)
Oryctolagus cuniculus (Rabbit)
(1)
1a
TIM-1r2rD01
D:6-244
1b
TIM-1r2rD02
D:6-244
1c
TIM-1r2rD03
D:6-244
1d
TIM-1r2rD04
D:6-244
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]
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Asymmetric Unit 1
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Asym.Unit (185 KB)
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