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4A1I
Asym. Unit
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
[
close entry info
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Hetero Components
(3, 38)
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
8
Ligand/Ion
CADMIUM ION
2
CL
8
Ligand/Ion
CHLORIDE ION
3
SO4
22
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(38, 38)
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)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:123 , SER A:136 , LYS A:137 , GLY A:138 , CYS A:139 , ARG A:141 , CD A:1169 , CL A:1170 , HOH A:2184 , HIS H:119
BINDING SITE FOR RESIDUE SO4 A1165
02
AC2
SOFTWARE
THR A:92 , ARG A:164 , HOH A:2157 , HOH A:2220 , HOH A:2221 , HOH A:2222 , HOH A:2223 , LEU D:12 , ASN H:13
BINDING SITE FOR RESIDUE SO4 A1166
03
AC3
SOFTWARE
ASN A:127 , VAL A:135 , ARG A:141 , HOH A:2190 , HOH A:2202
BINDING SITE FOR RESIDUE SO4 A1167
04
AC4
SOFTWARE
LEU A:12 , HOH A:2048 , HOH A:2049 , HOH A:2051 , HOH A:2224 , HOH A:2225 , THR D:92 , ARG D:164 , HOH E:2032
BINDING SITE FOR RESIDUE SO4 A1168
05
AC5
SOFTWARE
CYS A:139 , SO4 A:1165 , CL A:1170 , HOH A:2184 , HIS H:119
BINDING SITE FOR RESIDUE CD A1169
06
AC6
SOFTWARE
PHE A:108 , HIS A:119 , SO4 A:1165 , CD A:1169 , HOH A:2184 , HIS H:119
BINDING SITE FOR RESIDUE CL A1170
07
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
08
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
09
AC9
SOFTWARE
CYS B:139 , SO4 B:1165 , CL B:1168 , HOH B:2170
BINDING SITE FOR RESIDUE CD B1167
10
BC1
SOFTWARE
PHE B:108 , HIS B:119 , SO4 B:1165 , CD B:1167 , HOH B:2170
BINDING SITE FOR RESIDUE CL B1168
11
BC2
SOFTWARE
HIS C:123 , SER C:136 , LYS C:137 , GLY C:138 , CYS C:139 , ARG C:141 , CD C:1168 , CL C:1169 , HOH C:2173 , HOH C:2200 , HIS F:119
BINDING SITE FOR RESIDUE SO4 C1165
12
BC3
SOFTWARE
THR C:92 , ARG C:164 , HOH C:2149 , HOH C:2199 , HOH C:2201 , HOH C:2202 , HOH C:2203
BINDING SITE FOR RESIDUE SO4 C1166
13
BC4
SOFTWARE
ASN C:127 , VAL C:135 , ARG C:141 , HOH C:2184 , HOH C:2187
BINDING SITE FOR RESIDUE SO4 C1167
14
BC5
SOFTWARE
CYS C:139 , SO4 C:1165 , CL C:1169 , HOH C:2173 , HIS F:119
BINDING SITE FOR RESIDUE CD C1168
15
BC6
SOFTWARE
PHE C:108 , HIS C:119 , SO4 C:1165 , CD C:1168 , HOH C:2173 , HIS F:119 , HOH F:2128
BINDING SITE FOR RESIDUE CL C1169
16
BC7
SOFTWARE
HIS D:123 , SER D:136 , LYS D:137 , GLY D:138 , CYS D:139 , ARG D:141 , CD D:1166 , CL D:1167 , HOH D:2175 , HOH D:2211 , HIS E:119
BINDING SITE FOR RESIDUE SO4 D1165
17
BC8
SOFTWARE
CYS D:139 , SO4 D:1165 , CL D:1167 , HOH D:2175 , HIS E:119
BINDING SITE FOR RESIDUE CD D1166
18
BC9
SOFTWARE
PHE D:108 , TRP D:112 , HIS D:119 , SO4 D:1165 , CD D:1166 , HOH D:2175 , HIS E:119
BINDING SITE FOR RESIDUE CL D1167
19
CC1
SOFTWARE
HIS D:119 , HIS E:123 , SER E:136 , LYS E:137 , GLY E:138 , CYS E:139 , ARG E:141 , CD E:1168 , CL E:1169 , HOH E:2144 , HOH E:2169
BINDING SITE FOR RESIDUE SO4 E1165
20
CC2
SOFTWARE
ASN A:73 , ARG A:159 , HOH A:2121 , GLU E:94 , TYR E:96 , ARG E:159 , HOH E:2006
BINDING SITE FOR RESIDUE SO4 E1166
21
CC3
SOFTWARE
ASN E:127 , ARG E:141 , HOH E:2147
BINDING SITE FOR RESIDUE SO4 E1167
22
CC4
SOFTWARE
HIS D:119 , CYS E:139 , SO4 E:1165 , CL E:1169 , HOH E:2144
BINDING SITE FOR RESIDUE CD E1168
23
CC5
SOFTWARE
HIS D:119 , PHE E:108 , TRP E:112 , HIS E:119 , SO4 E:1165 , CD E:1168 , HOH E:2115 , HOH E:2144
BINDING SITE FOR RESIDUE CL E1169
24
CC6
SOFTWARE
HIS C:119 , HIS F:123 , SER F:136 , LYS F:137 , GLY F:138 , CYS F:139 , ARG F:141 , CD F:1168 , CL F:1169 , HOH F:2162 , HOH F:2192
BINDING SITE FOR RESIDUE SO4 F1165
25
CC7
SOFTWARE
TYR F:96 , ARG F:159 , HOH F:2005 , HOH F:2101 , HOH F:2194
BINDING SITE FOR RESIDUE SO4 F1166
26
CC8
SOFTWARE
ASN F:127 , ARG F:141 , HOH F:2163 , HOH F:2173
BINDING SITE FOR RESIDUE SO4 F1167
27
CC9
SOFTWARE
HIS C:119 , CYS F:139 , SO4 F:1165 , CL F:1169 , HOH F:2162
BINDING SITE FOR RESIDUE CD F1168
28
DC1
SOFTWARE
HIS C:119 , PHE F:108 , TRP F:112 , HIS F:119 , SO4 F:1165 , CD F:1168 , HOH F:2128 , HOH F:2162
BINDING SITE FOR RESIDUE CL F1169
29
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
30
DC3
SOFTWARE
ARG C:159 , TYR G:96 , ARG G:159 , HOH G:2005
BINDING SITE FOR RESIDUE SO4 G1166
31
DC4
SOFTWARE
ASN G:127 , ARG G:141 , HOH G:2136
BINDING SITE FOR RESIDUE SO4 G1167
32
DC5
SOFTWARE
CYS G:139 , SO4 G:1165 , CL G:1169 , HOH G:2133
BINDING SITE FOR RESIDUE CD G1168
33
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
34
DC7
SOFTWARE
HIS A:119 , HIS H:123 , SER H:136 , LYS H:137 , GLY H:138 , CYS H:139 , ARG H:141 , CD H:1168 , CL H:1169 , HOH H:2136 , HOH H:2166
BINDING SITE FOR RESIDUE SO4 H1165
35
DC8
SOFTWARE
ASN D:73 , ARG D:159 , HOH D:2114 , TYR H:96 , ARG H:159 , HOH H:2004 , HOH H:2112 , HOH H:2167
BINDING SITE FOR RESIDUE SO4 H1166
36
DC9
SOFTWARE
ASN H:127 , ARG H:141 , HOH H:2139 , HOH H:2168
BINDING SITE FOR RESIDUE SO4 H1167
37
EC1
SOFTWARE
HIS A:119 , CYS H:139 , SO4 H:1165 , CL H:1169 , HOH H:2136
BINDING SITE FOR RESIDUE CD H1168
38
EC2
SOFTWARE
HIS A:119 , LYS A:137 , PHE H:108 , TRP H:112 , HIS H:119 , SO4 H:1165 , CD H:1168 , HOH H:2136
BINDING SITE FOR RESIDUE CL H1169
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(1, 8)
Info
All PROSITE Patterns/Profiles
1: LYSM (A:2-45,B:2-45,C:2-45,D:2-45,E: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
8
A:2-45
B:2-45
C:2-45
D:2-45
E:2-45
F:2-45
G:2-45
H:2-45
[
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]
Exons
(0, 0)
Info
All Exons
View:
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Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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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Sorry, no Info available
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Label:
Sorry, no Info available
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Chain E
Chain F
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Chain H
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Asym.Unit (452 KB)
Header - Asym.Unit
Biol.Unit 1 (114 KB)
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Biol.Unit 2 (114 KB)
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Biol.Unit 3 (114 KB)
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