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1NZC
Biol. Unit 1
Info
Asym.Unit (291 KB)
Biol.Unit 1 (143 KB)
Biol.Unit 2 (143 KB)
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(1)
Title
:
THE HIGH RESOLUTION STRUCTURES OF RMLC FROM STREPTOCOCCUS SUIS IN COMPLEX WITH DTDP-D-XYLOSE
Authors
:
C. Dong, L. L. Major, A. Allen, W. Blankenfeldt, D. Maskell, J. H. Naismith
Date
:
17 Feb 03 (Deposition) - 24 Jun 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Jelly Roll-Like Structure; Beta Sheet, Isomerase
(Keyword Search:
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Reference
:
C. Dong, L. L. Major, A. Allen, W. Blankenfeldt, D. Maskell, J. H. Naismith
High-Resolution Structures Of Rmlc From Streptococcus Suis In Complex With Substrate Analogs Locate The Active Site Of This Class Of Enzyme
Structure V. 11 715 2003
(for further references see the
PDB file header
)
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Hetero Components
(1, 2)
Info
All Hetero Components
1a: NICKEL (II) ION (NIa)
1b: NICKEL (II) ION (NIb)
2a: THYMIDINE-5'-DIPHOSPHO-BETA-D-XYLO... (TDXa)
2b: THYMIDINE-5'-DIPHOSPHO-BETA-D-XYLO... (TDXb)
2c: THYMIDINE-5'-DIPHOSPHO-BETA-D-XYLO... (TDXc)
2d: THYMIDINE-5'-DIPHOSPHO-BETA-D-XYLO... (TDXd)
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No.
Name
Count
Type
Full Name
1
NI
-1
Ligand/Ion
NICKEL (II) ION
2
TDX
2
Ligand/Ion
THYMIDINE-5'-DIPHOSPHO-BETA-D-XYLOSE
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Sites
(4, 4)
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1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU B:52 , NI B:9603 , HOH B:9620 , HOH B:9632 , GLU C:52 , HOH C:9772 , HOH C:9814
BINDING SITE FOR RESIDUE NI C 9602
2
AC2
SOFTWARE
HOH B:9620 , HOH B:9632 , HOH B:9656 , GLY C:49 , NI C:9602 , HOH C:9642 , HOH C:9772
BINDING SITE FOR RESIDUE NI B 9603
3
AC3
SOFTWARE
ARG A:33 , PHE A:36 , GLU A:38 , HOH A:9064 , GLN B:61 , ARG B:73 , GLU B:78 , ASN B:127 , TYR B:140 , TRP B:146 , HOH B:9623 , HOH B:9624 , HOH B:9628 , HOH B:9636 , HOH B:9769
BINDING SITE FOR RESIDUE TDX B 9001
4
AC4
SOFTWARE
GLN A:61 , ASN A:63 , ARG A:73 , HIS A:76 , GLU A:78 , LYS A:82 , ASN A:127 , TYR A:140 , TRP A:146 , HOH A:9008 , HOH A:9010 , HOH A:9026 , HOH A:9028 , HOH A:9036 , HOH A:9040 , HOH A:9046 , HOH A:9071 , HOH A:9072 , HOH A:9096 , ARG B:33 , PHE B:36 , GLU B:38
BINDING SITE FOR RESIDUE TDX A 9002
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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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Exons
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SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1nzca_ (A:)
1b: SCOP_d1nzcc_ (C:)
1c: SCOP_d1nzcd_ (D:)
1d: SCOP_d1nzcb_ (B:)
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Protein Domains
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Organisms
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Class
:
All beta proteins
(24004)
Fold
:
Double-stranded beta-helix
(580)
Superfamily
:
RmlC-like cupins
(220)
Family
:
dTDP-sugar isomerase
(26)
Protein domain
:
dTDP-4-dehydrorhamnose 3,5-epimerase RmlC
(18)
Streptococcus suis [TaxId: 1307]
(4)
1a
d1nzca_
A:
1b
d1nzcc_
C:
1c
d1nzcd_
D:
1d
d1nzcb_
B:
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1nzcC00 (C:4-197)
1b: CATH_1nzcD00 (D:4-197)
1c: CATH_1nzcA00 (A:2-197)
1d: CATH_1nzcB00 (B:2-197)
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Organisms
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)
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Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Jelly Rolls
(1293)
Homologous Superfamily
:
Jelly Rolls
(177)
Streptococcus suis. Organism_taxid: 1307. Strain: serotype 2.
(3)
1a
1nzcC00
C:4-197
1b
1nzcD00
D:4-197
1c
1nzcA00
A:2-197
1d
1nzcB00
B:2-197
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_dTDP_sugar_isom_1nzcD01 (D:14-189)
1b: PFAM_dTDP_sugar_isom_1nzcD02 (D:14-189)
1c: PFAM_dTDP_sugar_isom_1nzcD03 (D:14-189)
1d: PFAM_dTDP_sugar_isom_1nzcD04 (D:14-189)
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Clan
:
Cupin
(179)
Family
:
dTDP_sugar_isom
(11)
Streptococcus suis
(3)
1a
dTDP_sugar_isom-1nzcD01
D:14-189
1b
dTDP_sugar_isom-1nzcD02
D:14-189
1c
dTDP_sugar_isom-1nzcD03
D:14-189
1d
dTDP_sugar_isom-1nzcD04
D:14-189
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Asymmetric Unit 1
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Show PDB file:
Asym.Unit (291 KB)
Header - Asym.Unit
Biol.Unit 1 (143 KB)
Header - Biol.Unit 1
Biol.Unit 2 (143 KB)
Header - Biol.Unit 2
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