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2XJA
Asym. Unit
Info
Asym.Unit (630 KB)
Biol.Unit 1 (160 KB)
Biol.Unit 2 (161 KB)
Biol.Unit 3 (161 KB)
Biol.Unit 4 (157 KB)
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(1)
Title
:
STRUCTURE OF MURE FROM M.TUBERCULOSIS WITH DIPEPTIDE AND ADP
Authors
:
C. Basavannacharya, P. R. Moody, S. Bhakta, N. Keep
Date
:
03 Jul 10 (Deposition) - 18 Aug 10 (Release) - 29 Dec 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Ligase, Peptidoglycan, Peptidase Ligase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Basavannacharya, P. R. Moody, T. Munshi, N. Cronin, N. H. Keep, S. Bhakta
Essential Residues For The Enzyme Activity Of Atp-Dependent Mure Ligase From Mycobacterium Tuberculosis.
Protein Cell V. 1 1011 2010
(for further references see the
PDB file header
)
[
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Hetero Components
(4, 22)
Info
All Hetero Components
1a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
1b: ADENOSINE-5'-DIPHOSPHATE (ADPb)
1c: ADENOSINE-5'-DIPHOSPHATE (ADPc)
1d: ADENOSINE-5'-DIPHOSPHATE (ADPd)
2a: LYSINE NZ-CARBOXYLIC ACID (KCXa)
2b: LYSINE NZ-CARBOXYLIC ACID (KCXb)
2c: LYSINE NZ-CARBOXYLIC ACID (KCXc)
2d: LYSINE NZ-CARBOXYLIC ACID (KCXd)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
3e: MAGNESIUM ION (MGe)
3f: MAGNESIUM ION (MGf)
3g: MAGNESIUM ION (MGg)
3h: MAGNESIUM ION (MGh)
3i: MAGNESIUM ION (MGi)
3j: MAGNESIUM ION (MGj)
4a: URIDINE-5'-DIPHOSPHATE-N-ACETYLMUR... (UAGa)
4b: URIDINE-5'-DIPHOSPHATE-N-ACETYLMUR... (UAGb)
4c: URIDINE-5'-DIPHOSPHATE-N-ACETYLMUR... (UAGc)
4d: URIDINE-5'-DIPHOSPHATE-N-ACETYLMUR... (UAGd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ADP
4
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
KCX
4
Mod. Amino Acid
LYSINE NZ-CARBOXYLIC ACID
3
MG
10
Ligand/Ion
MAGNESIUM ION
4
UAG
4
Ligand/Ion
URIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE-D-GLUTAMATE
[
close Hetero Component info
]
Sites
(18, 18)
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)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR A:154 , SER A:155 , GLY A:156 , LYS A:157 , THR A:158 , THR A:159 , GLU A:220 , ASN A:243 , TYR A:343 , ASN A:347 , ARG A:377 , LEU A:378 , ASP A:392 , ALA A:394 , SER A:402 , MG A:1534
BINDING SITE FOR RESIDUE ADP A1533
02
AC2
SOFTWARE
THR A:158 , THR A:180 , GLU A:220 , ADP A:1533 , HOH A:2001
BINDING SITE FOR RESIDUE MG A1534
03
AC3
SOFTWARE
ASP A:247 , HIS A:248 , KCX A:262 , UAG A:1536
BINDING SITE FOR RESIDUE MG A1535
04
AC4
SOFTWARE
LEU A:67 , ARG A:68 , ALA A:69 , GLN A:70 , GLY A:83 , SER A:84 , THR A:85 , THR A:86 , GLY A:88 , HIS A:91 , ARG A:128 , LEU A:194 , THR A:195 , THR A:196 , GLU A:198 , SER A:222 , LEU A:228 , ARG A:230 , HIS A:248 , MG A:1535 , HOH A:2001
BINDING SITE FOR RESIDUE UAG A1536
05
AC5
SOFTWARE
GLY B:140 , ASP D:215
BINDING SITE FOR RESIDUE MG B1533
06
AC6
SOFTWARE
THR B:154 , SER B:155 , GLY B:156 , LYS B:157 , THR B:158 , THR B:159 , THR B:180 , GLU B:220 , ASN B:243 , TYR B:343 , ASN B:347 , ARG B:377 , ASP B:392 , ALA B:394 , VAL B:403 , MG B:1535 , HOH B:2001
BINDING SITE FOR RESIDUE ADP B1534
07
AC7
SOFTWARE
THR B:158 , THR B:180 , GLU B:220 , ADP B:1534 , HOH B:2001
BINDING SITE FOR RESIDUE MG B1535
08
AC8
SOFTWARE
LEU B:67 , ARG B:68 , ALA B:69 , GLN B:70 , LEU B:81 , GLY B:83 , SER B:84 , THR B:85 , THR B:86 , GLY B:88 , HIS B:91 , LEU B:194 , THR B:195 , THR B:196 , GLU B:198 , SER B:222 , HIS B:224 , ARG B:230 , HIS B:248 , MG B:1537 , HOH B:2001
BINDING SITE FOR RESIDUE UAG B1536
09
AC9
SOFTWARE
LYS B:157 , HIS B:248 , KCX B:262 , UAG B:1536
BINDING SITE FOR RESIDUE MG B1537
10
BC1
SOFTWARE
SER C:155 , GLY C:156 , LYS C:157 , THR C:158 , THR C:159 , THR C:180 , GLU C:220 , ASN C:243 , TYR C:343 , ASN C:347 , ARG C:377 , LEU C:378 , ASP C:392 , ALA C:394 , SER C:402 , VAL C:403 , MG C:1534 , HOH C:2001
BINDING SITE FOR RESIDUE ADP C1533
11
BC2
SOFTWARE
THR C:158 , THR C:180 , GLU C:220 , ADP C:1533 , UAG C:1535 , HOH C:2001
BINDING SITE FOR RESIDUE MG C1534
12
BC3
SOFTWARE
LEU C:67 , ARG C:68 , ALA C:69 , GLN C:70 , LEU C:81 , GLY C:83 , SER C:84 , THR C:85 , THR C:86 , GLY C:88 , HIS C:91 , THR C:195 , THR C:196 , GLU C:198 , SER C:222 , HIS C:224 , ARG C:230 , HIS C:248 , MG C:1534 , MG C:1536 , HOH C:2001
BINDING SITE FOR RESIDUE UAG C1535
13
BC4
SOFTWARE
ASP C:247 , HIS C:248 , UAG C:1535
BINDING SITE FOR RESIDUE MG C1536
14
BC5
SOFTWARE
HIS D:395 , ASP D:448 , GLY D:502
BINDING SITE FOR RESIDUE MG D1533
15
BC6
SOFTWARE
SER D:155 , GLY D:156 , LYS D:157 , THR D:158 , THR D:159 , THR D:180 , GLU D:220 , ASN D:243 , TYR D:343 , ASN D:344 , ASN D:347 , ARG D:377 , LEU D:378 , ASP D:392 , ALA D:394 , SER D:402 , VAL D:403 , MG D:1535 , HOH D:2001
BINDING SITE FOR RESIDUE ADP D1534
16
BC7
SOFTWARE
THR D:158 , THR D:180 , GLU D:220 , ADP D:1534 , HOH D:2001
BINDING SITE FOR RESIDUE MG D1535
17
BC8
SOFTWARE
LEU D:67 , ARG D:68 , ALA D:69 , GLN D:70 , LEU D:81 , GLY D:83 , SER D:84 , THR D:85 , THR D:86 , GLY D:88 , HIS D:91 , LEU D:194 , THR D:195 , GLU D:198 , SER D:222 , HIS D:224 , ARG D:230 , HIS D:248 , MG D:1537 , HOH D:2001
BINDING SITE FOR RESIDUE UAG D1536
18
BC9
SOFTWARE
LYS D:157 , ASP D:247 , HIS D:248 , KCX D:262 , UAG D:1536
BINDING SITE FOR RESIDUE MG D1537
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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Sorry, no Info available
[
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Exons
(0, 0)
Info
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(0, 0)
Info
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Sorry, no Info available
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_2xjaA02 (A:142-375)
1b: CATH_2xjaB02 (B:142-375)
1c: CATH_2xjaC02 (C:142-375)
1d: CATH_2xjaD02 (D:142-375)
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(
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(
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(
)
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(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
(109)
Homologous Superfamily
:
[code=3.40.1190.10, no name defined]
(36)
Tb (Mycobacterium tuberculosis)
(1)
1a
2xjaA02
A:142-375
1b
2xjaB02
B:142-375
1c
2xjaC02
C:142-375
1d
2xjaD02
D:142-375
[
close CATH info
]
Pfam Domains
(3, 12)
Info
all PFAM domains
1a: PFAM_Mur_ligase_2xjaD01 (D:61-139)
1b: PFAM_Mur_ligase_2xjaD02 (D:61-139)
1c: PFAM_Mur_ligase_2xjaD03 (D:61-139)
1d: PFAM_Mur_ligase_2xjaD04 (D:61-139)
2a: PFAM_Mur_ligase_C_2xjaD05 (D:374-459)
2b: PFAM_Mur_ligase_C_2xjaD06 (D:374-459)
2c: PFAM_Mur_ligase_C_2xjaD07 (D:374-459)
2d: PFAM_Mur_ligase_C_2xjaD08 (D:374-459)
3a: PFAM_Mur_ligase_M_2xjaD09 (D:151-355)
3b: PFAM_Mur_ligase_M_2xjaD10 (D:151-355)
3c: PFAM_Mur_ligase_M_2xjaD11 (D:151-355)
3d: PFAM_Mur_ligase_M_2xjaD12 (D:151-355)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
NADP_Rossmann
(1239)
Family
:
Mur_ligase
(4)
Mycobacterium tuberculosis
(2)
1a
Mur_ligase-2xjaD01
D:61-139
1b
Mur_ligase-2xjaD02
D:61-139
1c
Mur_ligase-2xjaD03
D:61-139
1d
Mur_ligase-2xjaD04
D:61-139
Clan
:
no clan defined [family: Mur_ligase_C]
(24)
Family
:
Mur_ligase_C
(24)
Mycobacterium tuberculosis
(2)
2a
Mur_ligase_C-2xjaD05
D:374-459
2b
Mur_ligase_C-2xjaD06
D:374-459
2c
Mur_ligase_C-2xjaD07
D:374-459
2d
Mur_ligase_C-2xjaD08
D:374-459
Clan
:
no clan defined [family: Mur_ligase_M]
(23)
Family
:
Mur_ligase_M
(23)
Mycobacterium tuberculosis
(2)
3a
Mur_ligase_M-2xjaD09
D:151-355
3b
Mur_ligase_M-2xjaD10
D:151-355
3c
Mur_ligase_M-2xjaD11
D:151-355
3d
Mur_ligase_M-2xjaD12
D:151-355
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Asym.Unit (630 KB)
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