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4BUC
Biol. Unit 2
Info
Asym.Unit (307 KB)
Biol.Unit 1 (152 KB)
Biol.Unit 2 (150 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF MURD LIGASE FROM THERMOTOGA MARITIMA IN APO FORM
Authors
:
S. Favini-Stabile, C. Contreras-Martel, N. Thielens, A. Dessen
Date
:
20 Jun 13 (Deposition) - 17 Jul 13 (Release) - 18 Dec 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.17
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Ligase, Peptidoglycan Synthesis, Adp-Forming Enzyme, Cell Wall, Cell Shape, Cell Cycle, Nucleotide-Binding, Atp-Binding, Cell Division
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Favini-Stabile, C. Contreras-Martel, N. Thielens, A. Dessen
Mreb And Murg As Scaffolds For The Cytoplasmic Steps Of Peptidoglycan Biosynthesis
Environ. Microbiol. V. 15 3218 2013
[
close entry info
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Hetero Components
(5, 25)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
1e: CHLORIDE ION (CLe)
1f: CHLORIDE ION (CLf)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
3a: SELENOMETHIONINE (MSEa)
3b: SELENOMETHIONINE (MSEb)
3c: SELENOMETHIONINE (MSEc)
3d: SELENOMETHIONINE (MSEd)
3e: SELENOMETHIONINE (MSEe)
3f: SELENOMETHIONINE (MSEf)
3g: SELENOMETHIONINE (MSEg)
3h: SELENOMETHIONINE (MSEh)
3i: SELENOMETHIONINE (MSEi)
3j: SELENOMETHIONINE (MSEj)
3k: SELENOMETHIONINE (MSEk)
3l: SELENOMETHIONINE (MSEl)
3m: SELENOMETHIONINE (MSEm)
3n: SELENOMETHIONINE (MSEn)
3o: SELENOMETHIONINE (MSEo)
3p: SELENOMETHIONINE (MSEp)
3q: SELENOMETHIONINE (MSEq)
3r: SELENOMETHIONINE (MSEr)
3s: SELENOMETHIONINE (MSEs)
3t: SELENOMETHIONINE (MSEt)
3u: SELENOMETHIONINE (MSEu)
3v: SELENOMETHIONINE (MSEv)
3w: SELENOMETHIONINE (MSEw)
3x: SELENOMETHIONINE (MSEx)
4a: AMMONIUM ION (NH4a)
4b: AMMONIUM ION (NH4b)
5a: PHOSPHITE ION (PO3a)
5b: PHOSPHITE ION (PO3b)
6a: PHOSPHATE ION (PO4a)
6b: PHOSPHATE ION (PO4b)
6c: PHOSPHATE ION (PO4c)
6d: PHOSPHATE ION (PO4d)
6e: PHOSPHATE ION (PO4e)
6f: PHOSPHATE ION (PO4f)
6g: PHOSPHATE ION (PO4g)
6h: PHOSPHATE ION (PO4h)
6i: PHOSPHATE ION (PO4i)
6j: PHOSPHATE ION (PO4j)
6k: PHOSPHATE ION (PO4k)
6l: PHOSPHATE ION (PO4l)
6m: PHOSPHATE ION (PO4m)
6n: PHOSPHATE ION (PO4n)
6o: PHOSPHATE ION (PO4o)
6p: PHOSPHATE ION (PO4p)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
-1
Ligand/Ion
CHLORIDE ION
2
GOL
3
Ligand/Ion
GLYCEROL
3
MSE
12
Mod. Amino Acid
SELENOMETHIONINE
4
NH4
1
Ligand/Ion
AMMONIUM ION
5
PO3
1
Ligand/Ion
PHOSPHITE ION
6
PO4
8
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
]
Sites
(18, 18)
Info
All Sites
01: AC8 (SOFTWARE)
02: AC9 (SOFTWARE)
03: BC8 (SOFTWARE)
04: BC9 (SOFTWARE)
05: CC1 (SOFTWARE)
06: CC2 (SOFTWARE)
07: CC3 (SOFTWARE)
08: CC4 (SOFTWARE)
09: CC5 (SOFTWARE)
10: CC6 (SOFTWARE)
11: CC7 (SOFTWARE)
12: CC8 (SOFTWARE)
13: CC9 (SOFTWARE)
14: DC1 (SOFTWARE)
15: DC2 (SOFTWARE)
16: DC3 (SOFTWARE)
17: DC4 (SOFTWARE)
18: DC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC8
SOFTWARE
ALA A:52 , HIS A:75 , ILE A:91 , PO3 A:1008 , CL A:1402 , HOH A:2040 , ALA B:52 , GLY B:73 , GLY B:74 , HOH B:2017
BINDING SITE FOR RESIDUE PO4 A1007
02
AC9
SOFTWARE
SER A:96 , MSE A:97 , PO4 A:1007 , HOH A:2040 , GLY B:74 , HIS B:75 , SER B:96 , PO3 B:1008
BINDING SITE FOR RESIDUE PO3 A1008
03
BC8
SOFTWARE
LYS B:133 , SER B:177 , SER B:178 , PHE B:179 , ASP B:203 , TYR B:211 , LYS B:215 , HOH B:2031
BINDING SITE FOR RESIDUE PO4 B1000
04
BC9
SOFTWARE
GLY B:132 , THR B:135 , GLN B:278 , MSE B:279 , ASN B:282 , GOL B:1202
BINDING SITE FOR RESIDUE PO4 B1001
05
CC1
SOFTWARE
ASN B:196 , ASN B:231 , HIS B:233 , TYR B:277 , GLU B:281 , HOH B:2046 , HOH B:2047
BINDING SITE FOR RESIDUE PO4 B1002
06
CC2
SOFTWARE
ASP B:120 , LYS B:123 , GLU B:168 , HOH B:2024
BINDING SITE FOR RESIDUE PO4 B1003
07
CC3
SOFTWARE
LYS B:30 , SER B:31 , PRO B:89 , NH4 B:1501 , HOH B:2001 , HOH B:2002
BINDING SITE FOR RESIDUE PO4 B1004
08
CC4
SOFTWARE
ASP B:213 , ARG B:238 , GLU B:404 , MSE B:407 , HIS B:445 , HOH B:2057 , HOH B:2084
BINDING SITE FOR RESIDUE PO4 B1005
09
CC5
SOFTWARE
TYR B:86 , LYS B:107 , SER B:109 , PHE B:114 , ASP B:117 , GLU B:185
BINDING SITE FOR RESIDUE PO4 B1006
10
CC6
SOFTWARE
ALA A:52 , GLY A:73 , GLY A:74 , HOH A:2034 , ALA B:52 , HIS B:75 , ILE B:91 , PO3 B:1008 , CL B:1402 , HOH B:2020
BINDING SITE FOR RESIDUE PO4 B1007
11
CC7
SOFTWARE
GLY A:74 , HIS A:75 , SER A:96 , PO3 A:1008 , THR B:95 , SER B:96 , MSE B:97 , PO4 B:1007 , HOH B:2020
BINDING SITE FOR RESIDUE PO3 B1008
12
CC8
SOFTWARE
PHE B:182 , TRP B:183 , GLU B:397 , GLU B:401 , HOH B:2022
BINDING SITE FOR RESIDUE GOL B1200
13
CC9
SOFTWARE
ARG B:33 , LYS B:37 , GLU B:58 , PHE B:62
BINDING SITE FOR RESIDUE GOL B1201
14
DC1
SOFTWARE
GLY B:132 , LYS B:133 , SER B:134 , THR B:135 , PO4 B:1001
BINDING SITE FOR RESIDUE GOL B1202
15
DC2
SOFTWARE
GLU B:111 , GLY B:155 , PRO B:160 , ALA B:161 , GLN B:180
BINDING SITE FOR RESIDUE CL B1400
16
DC3
SOFTWARE
PHE B:28 , GLU B:51
BINDING SITE FOR RESIDUE CL B1401
17
DC4
SOFTWARE
GLY B:27 , GLU B:51 , ALA B:52 , HIS B:75 , PO4 B:1007
BINDING SITE FOR RESIDUE CL B1402
18
DC5
SOFTWARE
PO4 B:1004
BINDING SITE FOR RESIDUE NH4 B1501
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(, 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.
(no "Exon" information available for biological units yet)
SCOP Domains
(0, 0)
Info
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Sorry, no Info available
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CATH Domains
(0, 0)
Info
all CATH domains
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Label:
Sorry, no Info available
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
[
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Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain B
Asymmetric Unit 1
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Miscellaneous
Script
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)
ssbonds 100
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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Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
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Show PDB file:
Asym.Unit (307 KB)
Header - Asym.Unit
Biol.Unit 1 (152 KB)
Header - Biol.Unit 1
Biol.Unit 2 (150 KB)
Header - Biol.Unit 2
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