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2VBG
Asym. Unit
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Asym.Unit (197 KB)
Biol.Unit 1 (192 KB)
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(1)
Title
:
THE COMPLEX STRUCTURE OF THE BRANCHED-CHAIN KETO ACID DECARBOXYLASE (KDCA) FROM LACTOCOCCUS LACTIS WITH 2R-1-HYDROXYETHYL-DEAZATHDP
Authors
:
C. L. Berthold, D. Gocke, M. D. Wood, F. Leeper, M. Pohl, G. Schneider
Date
:
12 Sep 07 (Deposition) - 27 Nov 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Kdca, Flavoprotein, Thdp-Dependent Enzymes, Thiamine Pyrophosphate, Lyase
(Keyword Search:
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Reference
:
C. L. Berthold, D. Gocke, M. D. Wood, F. Leeper, M. Pohl, G. Schneider
Crystal Structure Of The Branched-Chain Keto Acid Decarboxylase (Kdca) From Lactococcus Lactis Provides Insights Into The Structural Basis For The Chemo- And Enantioselective Carboligation Reaction
Acta Crystallogr. , Sect. D V. 63 1217 2007
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Hetero Components
(2, 4)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
2a: 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5... (R1Ta)
2b: 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5... (R1Tb)
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No.
Name
Count
Type
Full Name
1
MG
2
Ligand/Ion
MAGNESIUM ION
2
R1T
2
Ligand/Ion
2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-[(1R)-1-HYDROXYETHYL]-3-METHYL-2-THIENYL}ETHYL TRIHYDROGEN DIPHOSPHATE
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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
ASP A:429 , ASN A:456 , GLY A:458 , R1T A:1549 , HOH A:2367
BINDING SITE FOR RESIDUE MG A1548
2
AC2
SOFTWARE
GLY A:378 , THR A:379 , GLY A:402 , SER A:403 , ILE A:404 , GLY A:428 , ASP A:429 , GLY A:430 , SER A:431 , ASN A:456 , GLY A:458 , TYR A:459 , THR A:460 , VAL A:461 , GLU A:462 , MG A:1548 , HOH A:2327 , HOH A:2367 , HOH A:2477 , HOH A:2478 , PRO B:24 , GLY B:25 , GLU B:49 , VAL B:74 , HIS B:113
BINDING SITE FOR RESIDUE R1T A1549
3
AC3
SOFTWARE
ASP B:429 , ASN B:456 , GLY B:458 , R1T B:1549 , HOH B:2374
BINDING SITE FOR RESIDUE MG B1548
4
AC4
SOFTWARE
PRO A:24 , GLY A:25 , GLU A:49 , VAL A:74 , HIS A:113 , GLY B:378 , THR B:379 , GLY B:402 , SER B:403 , ILE B:404 , GLY B:428 , ASP B:429 , GLY B:430 , SER B:431 , ASN B:456 , GLY B:458 , TYR B:459 , THR B:460 , VAL B:461 , GLU B:462 , MG B:1548 , HOH B:2374 , HOH B:2471 , HOH B:2472
BINDING SITE FOR RESIDUE R1T B1549
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SAPs(SNPs)/Variants
(0, 0)
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Exons
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SCOP Domains
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_2vbgA03 (A:351-540)
1b: CATH_2vbgB03 (B:351-540)
1c: CATH_2vbgA01 (A:-14-181)
1d: CATH_2vbgB01 (B:-14-181)
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Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.970, no name defined]
(144)
Lactococcus lactis. Organism_taxid: 1358.
(2)
1a
2vbgA03
A:351-540
1b
2vbgB03
B:351-540
1c
2vbgA01
A:-14-181
1d
2vbgB01
B:-14-181
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Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_TPP_enzyme_M_2vbgB01 (B:195-330)
1b: PFAM_TPP_enzyme_M_2vbgB02 (B:195-330)
2a: PFAM_TPP_enzyme_C_2vbgB03 (B:378-524)
2b: PFAM_TPP_enzyme_C_2vbgB04 (B:378-524)
3a: PFAM_TPP_enzyme_N_2vbgB05 (B:2-177)
3b: PFAM_TPP_enzyme_N_2vbgB06 (B:2-177)
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Clan
:
FAD_DHS
(82)
Family
:
TPP_enzyme_M
(50)
Lactococcus lactis
(1)
1a
TPP_enzyme_M-2vbgB01
B:195-330
1b
TPP_enzyme_M-2vbgB02
B:195-330
Clan
:
THDP-binding
(106)
Family
:
TPP_enzyme_C
(54)
Lactococcus lactis
(1)
2a
TPP_enzyme_C-2vbgB03
B:378-524
2b
TPP_enzyme_C-2vbgB04
B:378-524
Family
:
TPP_enzyme_N
(54)
Lactococcus lactis
(1)
3a
TPP_enzyme_N-2vbgB05
B:2-177
3b
TPP_enzyme_N-2vbgB06
B:2-177
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