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3M5V
Asym. Unit
Info
Asym.Unit (418 KB)
Biol.Unit 1 (410 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF DIHYDRODIPICOLINATE SYNTHASE FROM CAMPYLOBACTER JEJUNI
Authors
:
Y. Kim, M. Zhou, K. Kwon, W. F. Anderson, A. Joachimiak, Center For Str Genomics Of Infectious Diseases (Csgid)
Date
:
13 Mar 10 (Deposition) - 28 Apr 10 (Release) - 29 Feb 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Tim Barrel, Csgid, Amino-Acid Biosynthesis, Diaminopimelate Biosynthesis, Lyase, Lysine Biosynthesis, Schiff Base, Structural Genomics, Center For Structural Genomics Of Infectious Diseases
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Kim, M. Zhou, K. Kwon, W. F. Anderson, A. Joachimiak, Center For Structural Genomics Of Infectious Diseases (Csgid)
Crystal Structure Of Dihydrodipicolinate Synthase From Campylobacter Jejuni
To Be Published
[
close entry info
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Hetero Components
(5, 50)
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)
1g: CHLORIDE ION (CLg)
1h: CHLORIDE ION (CLh)
1i: CHLORIDE ION (CLi)
1j: CHLORIDE ION (CLj)
2a: FORMIC ACID (FMTa)
3a: SELENOMETHIONINE (MSEa)
3aa: SELENOMETHIONINE (MSEaa)
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)
3y: SELENOMETHIONINE (MSEy)
3z: SELENOMETHIONINE (MSEz)
4a: DI(HYDROXYETHYL)ETHER (PEGa)
4b: DI(HYDROXYETHYL)ETHER (PEGb)
4c: DI(HYDROXYETHYL)ETHER (PEGc)
5a: SULFATE ION (SO4a)
5b: SULFATE ION (SO4b)
5c: SULFATE ION (SO4c)
5d: SULFATE ION (SO4d)
5e: SULFATE ION (SO4e)
5f: SULFATE ION (SO4f)
5g: SULFATE ION (SO4g)
5h: SULFATE ION (SO4h)
5i: SULFATE ION (SO4i)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
10
Ligand/Ion
CHLORIDE ION
2
FMT
1
Ligand/Ion
FORMIC ACID
3
MSE
27
Mod. Amino Acid
SELENOMETHIONINE
4
PEG
3
Ligand/Ion
DI(HYDROXYETHYL)ETHER
5
SO4
9
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(21, 21)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:84 , TYR A:110 , HOH A:311 , HOH A:1131 , ASN C:84 , TYR C:110 , HOH C:347
BINDING SITE FOR RESIDUE SO4 A 301
02
AC2
SOFTWARE
ARG A:142 , PHE A:248 , SER A:251 , ASN A:252 , HOH A:496 , HOH A:1071 , HOH A:1144 , LYS C:113
BINDING SITE FOR RESIDUE SO4 A 302
03
AC3
SOFTWARE
ASN A:229 , TYR A:230 , LYS A:231 , GLU A:232
BINDING SITE FOR RESIDUE SO4 A 303
04
AC4
SOFTWARE
LYS A:280
BINDING SITE FOR RESIDUE CL A 304
05
AC5
SOFTWARE
THR A:115 , GLN A:116 , HOH A:328 , HOH A:613
BINDING SITE FOR RESIDUE SO4 A 305
06
AC6
SOFTWARE
ARG B:142 , PHE B:248 , SER B:251 , ASN B:252 , HOH B:447 , HOH B:884 , HOH B:1125 , HOH B:1127 , LYS D:113
BINDING SITE FOR RESIDUE SO4 B 302
07
AC7
SOFTWARE
THR B:115 , GLN B:116 , HOH B:1098 , HOH D:333
BINDING SITE FOR RESIDUE CL B 303
08
AC8
SOFTWARE
GLY B:46 , THR B:47 , ALA B:81 , GLY B:82 , LEU B:105 , VAL B:107 , TYR B:137 , LYS B:166 , HOH B:631 , HOH B:1136 , HOH B:1151
BINDING SITE FOR RESIDUE PEG B 305
09
AC9
SOFTWARE
ASN B:242
BINDING SITE FOR RESIDUE CL B 306
10
BC1
SOFTWARE
LYS C:280
BINDING SITE FOR RESIDUE CL C 301
11
BC2
SOFTWARE
HOH A:584 , THR C:115 , GLN C:116 , HOH C:1072 , HOH C:1105
BINDING SITE FOR RESIDUE CL C 302
12
BC3
SOFTWARE
SER C:277
BINDING SITE FOR RESIDUE CL C 303
13
BC4
SOFTWARE
LYS A:113 , ARG C:142 , PHE C:248 , SER C:251 , ASN C:252 , HOH C:365 , HOH C:1152 , HOH C:1154
BINDING SITE FOR RESIDUE SO4 C 304
14
BC5
SOFTWARE
GLY C:46 , THR C:47 , ALA C:81 , GLY C:82 , LEU C:105 , SER C:106 , VAL C:107 , TYR C:137 , LYS C:166 , HOH C:440 , HOH C:1132 , HOH C:1156
BINDING SITE FOR RESIDUE PEG C 305
15
BC6
SOFTWARE
ASN B:84 , TYR B:110 , ASN D:84 , TYR D:110 , HOH D:382
BINDING SITE FOR RESIDUE SO4 D 301
16
BC7
SOFTWARE
ASN D:229 , TYR D:230 , LYS D:231 , GLU D:232 , HOH D:509
BINDING SITE FOR RESIDUE SO4 D 299
17
BC8
SOFTWARE
LYS D:280
BINDING SITE FOR RESIDUE CL D 302
18
BC9
SOFTWARE
ARG D:60
BINDING SITE FOR RESIDUE CL D 303
19
CC1
SOFTWARE
HOH B:453 , THR D:115 , GLN D:116 , HOH D:1084
BINDING SITE FOR RESIDUE CL D 304
20
CC2
SOFTWARE
LYS B:113 , ARG D:142 , PHE D:248 , SER D:251 , ASN D:252 , HOH D:409 , HOH D:615 , HOH D:628
BINDING SITE FOR RESIDUE SO4 D 305
21
CC3
SOFTWARE
GLY D:46 , THR D:47 , GLY D:82 , LEU D:105 , SER D:106 , VAL D:107 , TYR D:137 , LYS D:166 , HOH D:448 , HOH D:522 , HOH D:1157
BINDING SITE FOR RESIDUE PEG D 306
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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
(2, 8)
Info
All PROSITE Patterns/Profiles
1: DHDPS_1 (A:41-58,B:41-58,C:41-58,D:41-58)
2: DHDPS_2 (A:137-168,B:137-168,C:137-168,D:13...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DHDPS_1
PS00665
Dihydrodipicolinate synthase signature 1.
DAPA_CAMJE
41-58
4
A:41-58
B:41-58
C:41-58
D:41-58
2
DHDPS_2
PS00666
Dihydrodipicolinate synthase signature 2.
DAPA_CAMJE
137-168
4
A:137-168
B:137-168
C:137-168
D:137-168
[
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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
(1, 4)
Info
All SCOP Domains
1a: SCOP_d3m5va_ (A:)
1b: SCOP_d3m5vb_ (B:)
1c: SCOP_d3m5vc_ (C:)
1d: SCOP_d3m5vd_ (D:)
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)
Protein Domains
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(
)
Organisms
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)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Aldolase
(457)
Family
:
automated matches
(113)
Protein domain
:
automated matches
(113)
Campylobacter jejuni [TaxId: 197]
(1)
1a
d3m5va_
A:
1b
d3m5vb_
B:
1c
d3m5vc_
C:
1d
d3m5vd_
D:
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_DHDPS_3m5vD01 (D:6-294)
1b: PFAM_DHDPS_3m5vD02 (D:6-294)
1c: PFAM_DHDPS_3m5vD03 (D:6-294)
1d: PFAM_DHDPS_3m5vD04 (D:6-294)
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(
)
(
)
Clan
:
TIM_barrel
(694)
Family
:
DHDPS
(40)
Campylobacter jejuni
(1)
1a
DHDPS-3m5vD01
D:6-294
1b
DHDPS-3m5vD02
D:6-294
1c
DHDPS-3m5vD03
D:6-294
1d
DHDPS-3m5vD04
D:6-294
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