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2YID
Asym. Unit
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Asym.Unit (1.1 MB)
Biol.Unit 1 (548 KB)
Biol.Unit 2 (556 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE SUCA DOMAIN OF MYCOBACTERIUM SMEGMATIS ALPHA-KETOGLUTARATE DECARBOXYLASE IN COMPLEX WITH THE ENAMINE-THDP INTERMEDIATE
Authors
:
T. Wagner, M. Bellinzoni, A. M. Wehenkel, H. M. O'Hare, P. M. Alzari
Date
:
11 May 11 (Deposition) - 15 Jun 11 (Release) - 12 Oct 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.25
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Lyase, Thdp-Covalent Adduct
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Wagner, M. Bellinzoni, A. M. Wehenkel, H. M. O'Hare, P. M. Alzari
Functional Plasticity And Allosteric Regulation Of Alpha-Ketoglutarate Decarboxylase In Central Mycobacterial Metabolism.
Chem. Biol. V. 18 1011 2011
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Hetero Components
(3, 12)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
3a: (4E)-4-{3-[(4-AMINO-2-METHYLPYRIMI... (TD7a)
3b: (4E)-4-{3-[(4-AMINO-2-METHYLPYRIMI... (TD7b)
3c: (4E)-4-{3-[(4-AMINO-2-METHYLPYRIMI... (TD7c)
3d: (4E)-4-{3-[(4-AMINO-2-METHYLPYRIMI... (TD7d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
4
Ligand/Ion
CALCIUM ION
2
MG
4
Ligand/Ion
MAGNESIUM ION
3
TD7
4
Ligand/Ion
(4E)-4-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-(2-{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-2(3H)-YLIDENE}-4-HYDROXYBUTANOIC ACID
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Sites
(12, 12)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PHE A:506 , HIS A:539 , ARG A:540 , TYR A:578 , HIS A:579 , SER A:604 , HIS A:605 , LEU A:606 , GLY A:644 , ASP A:645 , ALA A:646 , ALA A:647 , GLN A:651 , ASN A:678 , ILE A:680 , GLY A:681 , HIS A:747 , MG A:2002 , HOH A:3022 , HOH A:3024 , HOH A:3046 , HOH A:3047 , HOH A:3203 , GLN B:901 , LEU B:950 , GLU B:952 , GLN B:976 , PHE B:980 , HIS B:1020
BINDING SITE FOR RESIDUE TD7 A2001
02
AC2
SOFTWARE
ASP A:645 , ASN A:678 , ILE A:680 , TD7 A:2001 , HOH A:3047
BINDING SITE FOR RESIDUE MG A2002
03
AC3
SOFTWARE
ASP A:1004 , HIS A:1055 , ASP A:1058 , ILE A:1060 , HOH A:3153 , HOH A:3154
BINDING SITE FOR RESIDUE CA A2003
04
AC4
SOFTWARE
GLN A:901 , LEU A:950 , GLU A:952 , GLN A:976 , PHE A:980 , HIS A:1020 , PHE B:506 , HIS B:539 , ARG B:540 , TYR B:578 , HIS B:579 , SER B:604 , HIS B:605 , LEU B:606 , GLY B:644 , ASP B:645 , ALA B:646 , ALA B:647 , ASN B:678 , ILE B:680 , GLY B:681 , HIS B:747 , MG B:2002 , HOH B:3027 , HOH B:3028 , HOH B:3049 , HOH B:3050 , HOH B:3065
BINDING SITE FOR RESIDUE TD7 B2001
05
AC5
SOFTWARE
ASP B:645 , ASN B:678 , ILE B:680 , TD7 B:2001 , HOH B:3050
BINDING SITE FOR RESIDUE MG B2002
06
AC6
SOFTWARE
ASP B:1004 , HIS B:1055 , ASP B:1058 , ILE B:1060 , HOH B:3127 , HOH B:3128
BINDING SITE FOR RESIDUE CA B2003
07
AC7
SOFTWARE
HIS C:539 , ARG C:540 , TYR C:578 , HIS C:579 , SER C:604 , HIS C:605 , LEU C:606 , GLY C:644 , ASP C:645 , ALA C:646 , ALA C:647 , GLN C:651 , ASN C:678 , ILE C:680 , GLY C:681 , HIS C:747 , MG C:2002 , HOH C:3031 , HOH C:3032 , HOH C:3034 , HOH C:3061 , HOH C:3062 , GLN D:901 , LEU D:950 , GLU D:952 , GLN D:976 , PHE D:980 , HIS D:1020
BINDING SITE FOR RESIDUE TD7 C2001
08
AC8
SOFTWARE
ASP C:645 , ASN C:678 , ILE C:680 , TD7 C:2001 , HOH C:3062
BINDING SITE FOR RESIDUE MG C2002
09
AC9
SOFTWARE
ASP C:1004 , HIS C:1055 , ASP C:1058 , ILE C:1060 , HOH C:3177 , HOH C:3178
BINDING SITE FOR RESIDUE CA C2003
10
BC1
SOFTWARE
GLN C:901 , LEU C:950 , GLU C:952 , GLN C:976 , PHE C:980 , HIS C:1020 , HIS D:539 , ARG D:540 , TYR D:578 , HIS D:579 , SER D:604 , HIS D:605 , LEU D:606 , GLY D:644 , ASP D:645 , ALA D:646 , ALA D:647 , GLN D:651 , ASN D:678 , ILE D:680 , GLY D:681 , HIS D:747 , MG D:2002 , HOH D:3018 , HOH D:3019 , HOH D:3021 , HOH D:3037 , HOH D:3038
BINDING SITE FOR RESIDUE TD7 D2001
11
BC2
SOFTWARE
ASP D:645 , ASN D:678 , ILE D:680 , TD7 D:2001 , HOH D:3038
BINDING SITE FOR RESIDUE MG D2002
12
BC3
SOFTWARE
ASP D:1004 , HIS D:1055 , ASP D:1058 , ILE D:1060 , HOH D:3100 , HOH D:3101
BINDING SITE FOR RESIDUE CA D2003
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
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Exons
(0, 0)
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SCOP Domains
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CATH Domains
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Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_E1_dh_2yidD01 (D:484-816)
1b: PFAM_E1_dh_2yidD02 (D:484-816)
1c: PFAM_E1_dh_2yidD03 (D:484-816)
1d: PFAM_E1_dh_2yidD04 (D:484-816)
2a: PFAM_Transket_pyr_2yidD05 (D:874-1076)
2b: PFAM_Transket_pyr_2yidD06 (D:874-1076)
2c: PFAM_Transket_pyr_2yidD07 (D:874-1076)
2d: PFAM_Transket_pyr_2yidD08 (D:874-1076)
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Organisms
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(
)
Clan
:
THDP-binding
(106)
Family
:
E1_dh
(27)
Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
(5)
1a
E1_dh-2yidD01
D:484-816
1b
E1_dh-2yidD02
D:484-816
1c
E1_dh-2yidD03
D:484-816
1d
E1_dh-2yidD04
D:484-816
Family
:
Transket_pyr
(45)
Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
(5)
2a
Transket_pyr-2yidD05
D:874-1076
2b
Transket_pyr-2yidD06
D:874-1076
2c
Transket_pyr-2yidD07
D:874-1076
2d
Transket_pyr-2yidD08
D:874-1076
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Asym.Unit (1.1 MB)
Header - Asym.Unit
Biol.Unit 1 (548 KB)
Header - Biol.Unit 1
Biol.Unit 2 (556 KB)
Header - Biol.Unit 2
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