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4A1I
Biol. Unit 3
Info
Asym.Unit (452 KB)
Biol.Unit 1 (114 KB)
Biol.Unit 2 (114 KB)
Biol.Unit 3 (114 KB)
Biol.Unit 4 (115 KB)
Biol.Unit 5 (113 KB)
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(1)
Title
:
YKUD FROM B.SUBTILIS
Authors
:
M. Blaise, S. Fuglsang Midtgaard, S. Roi Midtgaard, T. Boesen, S. Thi
Date
:
15 Sep 11 (Deposition) - 26 Sep 12 (Release) - 03 Oct 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.76
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,H (1x)
Biol. Unit 2: B,G (1x)
Biol. Unit 3: B,G (1x)
Biol. Unit 4: C,F (1x)
Biol. Unit 5: D,E (1x)
Keywords
:
Transferase, Peptidoglycan Synthesis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Blaise, S. Fuglsang Midtgaard, S. Roi Midtgaard, T. Boesen, S. Thirup
Structures Of Three New Crystal Forms Of The Ykud L, D-Transpeptidase From B. Subtilis.
To Be Published
[
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Hetero Components
(1, 2)
Info
All Hetero Components
1a: CADMIUM ION (CDa)
1b: CADMIUM ION (CDb)
1c: CADMIUM ION (CDc)
1d: CADMIUM ION (CDd)
1e: CADMIUM ION (CDe)
1f: CADMIUM ION (CDf)
1g: CADMIUM ION (CDg)
1h: CADMIUM ION (CDh)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
2e: CHLORIDE ION (CLe)
2f: CHLORIDE ION (CLf)
2g: CHLORIDE ION (CLg)
2h: CHLORIDE ION (CLh)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
3f: SULFATE ION (SO4f)
3g: SULFATE ION (SO4g)
3h: SULFATE ION (SO4h)
3i: SULFATE ION (SO4i)
3j: SULFATE ION (SO4j)
3k: SULFATE ION (SO4k)
3l: SULFATE ION (SO4l)
3m: SULFATE ION (SO4m)
3n: SULFATE ION (SO4n)
3o: SULFATE ION (SO4o)
3p: SULFATE ION (SO4p)
3q: SULFATE ION (SO4q)
3r: SULFATE ION (SO4r)
3s: SULFATE ION (SO4s)
3t: SULFATE ION (SO4t)
3u: SULFATE ION (SO4u)
3v: SULFATE ION (SO4v)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CD
-1
Ligand/Ion
CADMIUM ION
2
CL
-1
Ligand/Ion
CHLORIDE ION
3
SO4
2
Ligand/Ion
SULFATE ION
[
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Sites
(9, 9)
Info
All Sites
1: AC7 (SOFTWARE)
2: AC8 (SOFTWARE)
3: AC9 (SOFTWARE)
4: BC1 (SOFTWARE)
5: DC2 (SOFTWARE)
6: DC3 (SOFTWARE)
7: DC4 (SOFTWARE)
8: DC5 (SOFTWARE)
9: DC6 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC7
SOFTWARE
HIS B:123 , SER B:136 , LYS B:137 , GLY B:138 , CYS B:139 , ARG B:141 , CD B:1167 , CL B:1168 , HOH B:2170
BINDING SITE FOR RESIDUE SO4 B1165
2
AC8
SOFTWARE
THR B:92 , ARG B:164 , HOH B:2202 , HOH B:2203 , HOH B:2204 , HOH B:2205
BINDING SITE FOR RESIDUE SO4 B1166
3
AC9
SOFTWARE
CYS B:139 , SO4 B:1165 , CL B:1168 , HOH B:2170
BINDING SITE FOR RESIDUE CD B1167
4
BC1
SOFTWARE
PHE B:108 , HIS B:119 , SO4 B:1165 , CD B:1167 , HOH B:2170
BINDING SITE FOR RESIDUE CL B1168
5
DC2
SOFTWARE
HIS G:123 , SER G:136 , LYS G:137 , GLY G:138 , CYS G:139 , ARG G:141 , CD G:1168 , CL G:1169 , HOH G:2133 , HOH G:2160 , HOH G:2161
BINDING SITE FOR RESIDUE SO4 G1165
6
DC3
SOFTWARE
ARG C:159 , TYR G:96 , ARG G:159 , HOH G:2005
BINDING SITE FOR RESIDUE SO4 G1166
7
DC4
SOFTWARE
ASN G:127 , ARG G:141 , HOH G:2136
BINDING SITE FOR RESIDUE SO4 G1167
8
DC5
SOFTWARE
CYS G:139 , SO4 G:1165 , CL G:1169 , HOH G:2133
BINDING SITE FOR RESIDUE CD G1168
9
DC6
SOFTWARE
PHE G:108 , TRP G:112 , HIS G:119 , SO4 G:1165 , CD G:1168 , HOH G:2102 , HOH G:2133
BINDING SITE FOR RESIDUE CL G1169
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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
(1, 2)
Info
All PROSITE Patterns/Profiles
1: LYSM (B:2-45,G:2-45)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
LYSM
PS51782
LysM domain profile.
YKUD_BACSU
2-45
2
-
B:2-45
-
-
-
-
G:2-45
-
[
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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
(2, 16)
Info
All SCOP Domains
1a: SCOP_d4a1ia2 (A:49-164)
1b: SCOP_d4a1ib2 (B:49-164)
1c: SCOP_d4a1ic2 (C:49-164)
1d: SCOP_d4a1id2 (D:49-164)
1e: SCOP_d4a1ie2 (E:49-164)
1f: SCOP_d4a1if2 (F:49-164)
1g: SCOP_d4a1ig2 (G:49-164)
1h: SCOP_d4a1ih2 (H:49-164)
2a: SCOP_d4a1ia1 (A:0-48)
2b: SCOP_d4a1ib1 (B:0-48)
2c: SCOP_d4a1ic1 (C:0-48)
2d: SCOP_d4a1id1 (D:0-48)
2e: SCOP_d4a1ie1 (E:1-48)
2f: SCOP_d4a1if1 (F:1-48)
2g: SCOP_d4a1ig1 (G:1-48)
2h: SCOP_d4a1ih1 (H:1-48)
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Classes
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(
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Folds
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)
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Families
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
L,D-transpeptidase catalytic domain-like
(8)
Superfamily
:
L,D-transpeptidase catalytic domain-like
(8)
Family
:
L,D-transpeptidase catalytic domain-like
(8)
Protein domain
:
automated matches
(5)
Bacillus subtilis [TaxId: 1423]
(3)
1a
d4a1ia2
A:49-164
1b
d4a1ib2
B:49-164
1c
d4a1ic2
C:49-164
1d
d4a1id2
D:49-164
1e
d4a1ie2
E:49-164
1f
d4a1if2
F:49-164
1g
d4a1ig2
G:49-164
1h
d4a1ih2
H:49-164
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
LysM domain
(7)
Superfamily
:
LysM domain
(7)
Family
:
automated matches
(5)
Protein domain
:
automated matches
(5)
Bacillus subtilis [TaxId: 1423]
(3)
2a
d4a1ia1
A:0-48
2b
d4a1ib1
B:0-48
2c
d4a1ic1
C:0-48
2d
d4a1id1
D:0-48
2e
d4a1ie1
E:1-48
2f
d4a1if1
F:1-48
2g
d4a1ig1
G:1-48
2h
d4a1ih1
H:1-48
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
View:
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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
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Protein & NOT Site
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Chain B
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Asymmetric Unit 1
Asymmetric Unit 2
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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Show PDB file:
Asym.Unit (452 KB)
Header - Asym.Unit
Biol.Unit 1 (114 KB)
Header - Biol.Unit 1
Biol.Unit 2 (114 KB)
Header - Biol.Unit 2
Biol.Unit 3 (114 KB)
Header - Biol.Unit 3
Biol.Unit 4 (115 KB)
Header - Biol.Unit 4
Biol.Unit 5 (113 KB)
Header - Biol.Unit 5
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