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1SJD
Biol. Unit 1
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Asym.Unit (256 KB)
Biol.Unit 1 (494 KB)
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(1)
Title
:
X-RAY STRUCTURE OF O-SUCCINYLBENZOATE SYNTHASE COMPLEXED WITH N-SUCCINYL PHENYLGLYCINE
Authors
:
J. B. Thoden, E. A. Taylor-Ringia, J. B. Garrett, J. A. Gerlt, H. M. Holden, I. Rayment
Date
:
03 Mar 04 (Deposition) - 01 Jun 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.87
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (2x)
Keywords
:
Racemase, Lyase, Isomerase
(Keyword Search:
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)
Reference
:
J. B. Thoden, E. A. Taylor-Ringia, J. B. Garrett, J. A. Gerlt, H. M. Holden, I. Rayment
Evolution Of Enzymatic Activity In The Enolase Superfamily: Structural Studies Of The Promiscuous O-Succinylbenzoate Synthase From Amycolatopsis
Biochemistry V. 43 5716 2004
(for further references see the
PDB file header
)
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Hetero Components
(1, 12)
Info
All Hetero Components
1a: N-SUCCINYL PHENYLGLYCINE (NPGa)
1b: N-SUCCINYL PHENYLGLYCINE (NPGb)
1c: N-SUCCINYL PHENYLGLYCINE (NPGc)
1d: N-SUCCINYL PHENYLGLYCINE (NPGd)
1e: N-SUCCINYL PHENYLGLYCINE (NPGe)
1f: N-SUCCINYL PHENYLGLYCINE (NPGf)
View:
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Label:
No.
Name
Count
Type
Full Name
1
NPG
12
Ligand/Ion
N-SUCCINYL PHENYLGLYCINE
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Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
MET A:50 , SER A:135 , LYS A:161 , LYS A:163 , ASN A:191 , LYS A:263 , GLY A:291 , MET A:292 , ILE A:293 , ASP A:316 , PHE A:323 , HOH A:1201 , HOH A:1222 , HOH A:1303 , HOH A:1382
BINDING SITE FOR RESIDUE NPG A 1200
2
AC2
SOFTWARE
PHE B:23 , MET B:50 , SER B:135 , LYS B:163 , ASN B:191 , LYS B:263 , GLY B:291 , MET B:292 , ILE B:293 , ASP B:316 , PHE B:323 , HOH B:1301 , HOH B:1330 , HOH B:1560 , HOH B:1561
BINDING SITE FOR RESIDUE NPG B 1300
3
AC3
SOFTWARE
MET C:50 , SER C:135 , LYS C:161 , LYS C:163 , ASN C:191 , LYS C:263 , GLY C:291 , MET C:292 , ILE C:293 , ASP C:316 , PHE C:323 , HOH C:1401 , HOH C:1418 , HOH C:1468 , HOH C:1582
BINDING SITE FOR RESIDUE NPG C 1400
4
AC4
SOFTWARE
MET D:50 , SER D:135 , LYS D:161 , LYS D:163 , ASN D:191 , ASP D:239 , LYS D:263 , GLY D:291 , MET D:292 , ILE D:293 , ASP D:316 , PHE D:323
BINDING SITE FOR RESIDUE NPG D 1500
5
AC5
SOFTWARE
ASP A:61 , GLY A:62 , HIS A:65 , ASP B:61 , GLY B:62 , HIS B:65 , ARG B:68 , HIS B:69 , HOH B:1341 , HOH B:1403 , HOH B:1657
BINDING SITE FOR RESIDUE NPG B 1163
6
AC6
SOFTWARE
ASP C:61 , GLY C:62 , HIS C:65 , HOH C:1711 , HOH C:1728 , ASP D:61 , GLY D:62 , HIS D:65 , HIS D:69 , HOH D:1547
BINDING SITE FOR RESIDUE NPG C 1164
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(, 0)
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Exons
(0, 0)
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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
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1sjda2 (A:1-125)
1b: SCOP_d1sjdb2 (B:1-125)
1c: SCOP_d1sjdc2 (C:1-125)
1d: SCOP_d1sjdd2 (D:1-125)
2a: SCOP_d1sjda1 (A:126-367)
2b: SCOP_d1sjdb1 (B:126-368)
2c: SCOP_d1sjdc1 (C:126-367)
2d: SCOP_d1sjdd1 (D:126-367)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Enolase N-terminal domain-like
(211)
Superfamily
:
Enolase N-terminal domain-like
(211)
Family
:
Enolase N-terminal domain-like
(88)
Protein domain
:
N-acylamino acid racemase
(10)
Amycolatopsis sp. [TaxId: 37632]
(4)
1a
d1sjda2
A:1-125
1b
d1sjdb2
B:1-125
1c
d1sjdc2
C:1-125
1d
d1sjdd2
D:1-125
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Enolase C-terminal domain-like
(212)
Family
:
D-glucarate dehydratase-like
(65)
Protein domain
:
N-acylamino acid racemase
(10)
Amycolatopsis sp. [TaxId: 37632]
(4)
2a
d1sjda1
A:126-367
2b
d1sjdb1
B:126-368
2c
d1sjdc1
C:126-367
2d
d1sjdd1
D:126-367
[
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1sjdA02 (A:116-352)
1b: CATH_1sjdB02 (B:116-352)
1c: CATH_1sjdC02 (C:116-352)
1d: CATH_1sjdD02 (D:116-352)
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Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Enolase superfamily
(142)
Amycolatopsis sp.. Organism_taxid: 37632.
(4)
1a
1sjdA02
A:116-352
1b
1sjdB02
B:116-352
1c
1sjdC02
C:116-352
1d
1sjdD02
D:116-352
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Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_MR_MLE_N_1sjdD01 (D:4-124)
1b: PFAM_MR_MLE_N_1sjdD02 (D:4-124)
1c: PFAM_MR_MLE_N_1sjdD03 (D:4-124)
1d: PFAM_MR_MLE_N_1sjdD04 (D:4-124)
2a: PFAM_MR_MLE_1sjdD05 (D:172-239)
2b: PFAM_MR_MLE_1sjdD06 (D:172-239)
2c: PFAM_MR_MLE_1sjdD07 (D:172-239)
2d: PFAM_MR_MLE_1sjdD08 (D:172-239)
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)
Clan
:
Enolase_N
(69)
Family
:
MR_MLE_N
(47)
Amycolatopsis sp
(4)
1a
MR_MLE_N-1sjdD01
D:4-124
1b
MR_MLE_N-1sjdD02
D:4-124
1c
MR_MLE_N-1sjdD03
D:4-124
1d
MR_MLE_N-1sjdD04
D:4-124
Clan
:
Enolase_TIM
(82)
Family
:
MR_MLE
(48)
Amycolatopsis sp
(4)
2a
MR_MLE-1sjdD05
D:172-239
2b
MR_MLE-1sjdD06
D:172-239
2c
MR_MLE-1sjdD07
D:172-239
2d
MR_MLE-1sjdD08
D:172-239
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Asym.Unit (256 KB)
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