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3FSX
Asym. Unit
Info
Asym.Unit (239 KB)
Biol.Unit 1 (142 KB)
Biol.Unit 2 (145 KB)
Biol.Unit 3 (131 KB)
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(1)
Title
:
STRUCTURE OF TETRAHYDRODIPICOLINATE N-SUCCINYLTRANSFERASE (RV1201C; DAPD) FROM MYCOBACTERIUM TUBERCULOSIS
Authors
:
L. Schuldt, S. Weyand, G. Kefala, M. S. Weiss
Date
:
12 Jan 09 (Deposition) - 23 Jun 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.15
Chains
:
Asym. Unit : A,B,C,D,E
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: D (3x)
Biol. Unit 3: E (3x)
Keywords
:
Beta Helix, L Beta H Domain, Acyltransferase, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. Schuldt, S. Weyand, G. Kefala, M. S. Weiss
The Three-Dimensional Structure Of A Mycobacterial Dapd Provides Insights Into Dapd Diversity And Reveals Unexpecte Particulars About The Enzymatic Mechanism.
J. Mol. Biol. V. 389 863 2009
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Hetero Components
(4, 20)
Info
All Hetero Components
1a: ACETIC ACID (ACYa)
1b: ACETIC ACID (ACYb)
1c: ACETIC ACID (ACYc)
1d: ACETIC ACID (ACYd)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
2e: MAGNESIUM ION (MGe)
2f: MAGNESIUM ION (MGf)
2g: MAGNESIUM ION (MGg)
2h: MAGNESIUM ION (MGh)
2i: MAGNESIUM ION (MGi)
3a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
3b: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDb)
3c: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDc)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
4c: SODIUM ION (NAc)
4d: SODIUM ION (NAd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACY
4
Ligand/Ion
ACETIC ACID
2
MG
9
Ligand/Ion
MAGNESIUM ION
3
MPD
3
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
4
NA
4
Ligand/Ion
SODIUM ION
[
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Sites
(20, 20)
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)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:201 , SER A:203 , SER A:219 , GLY C:216
BINDING SITE FOR RESIDUE ACY A 331
02
AC2
SOFTWARE
HIS A:94 , ARG A:95 , VAL A:156 , PRO A:157 , THR A:158 , HOH A:406
BINDING SITE FOR RESIDUE MPD A 340
03
AC3
SOFTWARE
ALA A:242 , ARG B:201 , SER B:203 , SER B:219 , ILE B:220 , GLY B:222 , HOH B:466
BINDING SITE FOR RESIDUE ACY B 331
04
AC4
SOFTWARE
HIS B:94 , ARG B:95 , VAL B:156 , PRO B:157 , THR B:158 , HOH B:485 , HOH B:543
BINDING SITE FOR RESIDUE MPD B 340
05
AC5
SOFTWARE
ALA B:242 , ARG C:201 , SER C:203 , SER C:219 , ILE C:220 , GLY C:222 , HOH C:486 , HOH C:511
BINDING SITE FOR RESIDUE ACY C 331
06
AC6
SOFTWARE
ARG D:201 , SER D:203 , GLY D:216 , SER D:219 , ILE D:220 , GLY D:222 , ALA D:242
BINDING SITE FOR RESIDUE ACY D 331
07
AC7
SOFTWARE
HIS D:94 , ARG D:95 , VAL D:156 , PRO D:157 , THR D:158
BINDING SITE FOR RESIDUE MPD D 340
08
AC8
SOFTWARE
ASP A:166 , NA A:334 , HOH A:401 , ASP B:166 , HOH B:401 , ASP C:166 , HOH C:401
BINDING SITE FOR RESIDUE MG C 332
09
AC9
SOFTWARE
GLU A:183 , GLU B:183 , GLU C:183
BINDING SITE FOR RESIDUE MG A 332
10
BC1
SOFTWARE
ASP D:166 , NA D:334 , HOH D:401
BINDING SITE FOR RESIDUE MG D 332
11
BC2
SOFTWARE
GLU D:183
BINDING SITE FOR RESIDUE MG D 333
12
BC3
SOFTWARE
ASP E:166
BINDING SITE FOR RESIDUE MG E 331
13
BC4
SOFTWARE
GLU E:183
BINDING SITE FOR RESIDUE MG E 332
14
BC5
SOFTWARE
HOH A:512 , HOH A:519 , HOH D:541
BINDING SITE FOR RESIDUE MG A 333
15
BC6
SOFTWARE
HOH D:511 , SER E:295
BINDING SITE FOR RESIDUE MG E 333
16
BC7
SOFTWARE
HOH B:534 , HOH B:547
BINDING SITE FOR RESIDUE MG B 332
17
BC8
SOFTWARE
ASP A:164 , ASP A:166 , ASP B:164 , ASP B:166 , ASP C:164 , ASP C:166 , MG C:332
BINDING SITE FOR RESIDUE NA A 334
18
BC9
SOFTWARE
ASP D:164 , ASP D:166 , MG D:332
BINDING SITE FOR RESIDUE NA D 334
19
CC1
SOFTWARE
ASP E:164 , ASP E:166
BINDING SITE FOR RESIDUE NA E 334
20
CC2
SOFTWARE
ASP B:210
BINDING SITE FOR RESIDUE NA B 333
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
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End label:
Sorry, no Info available
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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
All SCOP Domains
View:
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Sorry, no Info available
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CATH Domains
(2, 10)
Info
all CATH domains
1a: CATH_3fsxA02 (A:111-150)
1b: CATH_3fsxB02 (B:111-150)
1c: CATH_3fsxC02 (C:111-150)
1d: CATH_3fsxD02 (D:111-150)
1e: CATH_3fsxE02 (E:111-150)
2a: CATH_3fsxD03 (D:151-310)
2b: CATH_3fsxB03 (B:151-309)
2c: CATH_3fsxA03 (A:151-310)
2d: CATH_3fsxC03 (C:151-303)
2e: CATH_3fsxE03 (E:151-303)
View:
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Classes
(
)
(
)
Architectures
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)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Wheat Germ Agglutinin (Isolectin 2); domain 1
(140)
Homologous Superfamily
:
Trimeric LpxA-like enzymes
(3)
Mycobacterium tuberculosis. Organism_taxid: 83332. Strain: h37rv.
(2)
1a
3fsxA02
A:111-150
1b
3fsxB02
B:111-150
1c
3fsxC02
C:111-150
1d
3fsxD02
D:111-150
1e
3fsxE02
E:111-150
Class
:
Mainly Beta
(13760)
Architecture
:
3 Solenoid
(196)
Topology
:
UDP N-Acetylglucosamine Acyltransferase; domain 1
(90)
Homologous Superfamily
:
Hexapeptide repeat proteins
(85)
Mycobacterium tuberculosis. Organism_taxid: 83332. Strain: h37rv.
(2)
2a
3fsxD03
D:151-310
2b
3fsxB03
B:151-309
2c
3fsxA03
A:151-310
2d
3fsxC03
C:151-303
2e
3fsxE03
E:151-303
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Asymmetric Unit 1
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Miscellaneous
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Example Commands
Example Command
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select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
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show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
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Asym.Unit (239 KB)
Header - Asym.Unit
Biol.Unit 1 (142 KB)
Header - Biol.Unit 1
Biol.Unit 2 (145 KB)
Header - Biol.Unit 2
Biol.Unit 3 (131 KB)
Header - Biol.Unit 3
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