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3PB2
Biol. Unit 1
Info
Asym.Unit (313 KB)
Biol.Unit 1 (208 KB)
Biol.Unit 2 (195 KB)
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(1)
Title
:
CHARACTERISATION OF THE FIRST MONOMERIC DIHYDRODIPICOLINATE SYNTHASE VARIANT REVEALS EVOLUTIONARY INSIGHTS
Authors
:
F. G. Pearce, R. C. J. Dobson, G. B. Jameson
Date
:
20 Oct 10 (Deposition) - 23 Nov 11 (Release) - 28 Aug 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,E (1x)
Biol. Unit 2: D,F (2x)
Keywords
:
Tim-Barrel, Lyase
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
F. G. Pearce, R. C. Dobson, G. B. Jameson, M. A. Perugini, J. A. Gerrard
Characterization Of Monomeric Dihydrodipicolinate Synthase Variant Reveals The Importance Of Substrate Binding In Optimizing Oligomerization.
Biochim. Biophys. Acta V. 1814 1900 2011
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Hetero Components
(1, 14)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
1e: GLYCEROL (GOLe)
1f: GLYCEROL (GOLf)
1g: GLYCEROL (GOLg)
1h: GLYCEROL (GOLh)
1i: GLYCEROL (GOLi)
1j: GLYCEROL (GOLj)
1k: GLYCEROL (GOLk)
1l: GLYCEROL (GOLl)
1m: GLYCEROL (GOLm)
1n: GLYCEROL (GOLn)
1o: GLYCEROL (GOLo)
View:
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Label:
No.
Name
Count
Type
Full Name
1
GOL
14
Ligand/Ion
GLYCEROL
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Sites
(14, 14)
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)
View:
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR A:120 , HOH A:383 , GLU B:17 , LEU B:271 , HOH B:340 , HOH B:487
BINDING SITE FOR RESIDUE GOL A 295
02
AC2
SOFTWARE
LYS A:119 , TYR A:120 , GLU A:123 , ARG A:124 , HOH A:340 , HOH A:410 , LYS B:14 , HOH B:487
BINDING SITE FOR RESIDUE GOL A 296
03
AC3
SOFTWARE
VAL A:134 , ARG A:137 , GLY A:189 , PHE A:247 , ASN A:251 , HOH A:391 , HOH A:717
BINDING SITE FOR RESIDUE GOL A 297
04
AC4
SOFTWARE
TYR A:224 , GLY A:227 , ARG C:28 , GLU E:230
BINDING SITE FOR RESIDUE GOL A 298
05
AC5
SOFTWARE
PRO A:135 , VAL A:140 , ASN A:141 , HOH A:406 , HOH A:485 , HOH A:936
BINDING SITE FOR RESIDUE GOL A 299
06
AC6
SOFTWARE
ALA A:200 , HOH A:452 , HOH A:461 , HOH A:688 , HOH A:897 , HOH A:1012
BINDING SITE FOR RESIDUE GOL A 300
07
AC7
SOFTWARE
TYR B:132 , ARG B:137 , ALA B:163 , GLY B:189 , PHE B:247 , ASN B:251 , HOH B:787 , HOH B:1003 , HOH B:1063
BINDING SITE FOR RESIDUE GOL B 295
08
AC8
SOFTWARE
GLU B:32 , LYS B:215 , GLU B:223
BINDING SITE FOR RESIDUE GOL B 296
09
AC9
SOFTWARE
TYR A:106 , HOH A:368 , SER B:47 , PRO B:48 , GLY B:77 , HOH B:755 , HOH B:861
BINDING SITE FOR RESIDUE GOL B 297
10
BC1
SOFTWARE
TYR A:120 , ARG A:124 , HOH A:326 , HOH A:428 , HOH A:745 , GLU B:17 , LEU B:18 , LYS B:57 , HOH B:604
BINDING SITE FOR RESIDUE GOL B 298
11
BC2
SOFTWARE
TYR C:224 , GLY C:227 , LEU C:229
BINDING SITE FOR RESIDUE GOL C 295
12
BC3
SOFTWARE
TYR C:132 , ARG C:137 , LYS C:161 , GLY C:189 , PHE C:247 , ASN C:251 , HOH C:727
BINDING SITE FOR RESIDUE GOL C 296
13
BC4
SOFTWARE
GLY C:4 , VAL C:5 , ASN C:36 , VAL C:218 , CYS C:221 , ALA C:222 , PHE C:225 , HOH C:412 , HOH C:785
BINDING SITE FOR RESIDUE GOL C 297
14
BC5
SOFTWARE
TYR C:29 , ALA C:213 , PRO C:214 , LYS C:215 , GLN C:216 , LEU C:293 , HOH C:334 , HOH C:856 , HOH C:860
BINDING SITE FOR RESIDUE GOL C 298
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: DHDPS_1 (A:37-54,B:37-54,C:37-54,E:37-54)
2: DHDPS_2 (A:132-163,B:132-163,C:132-163,E:13...)
;
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PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DHDPS_1
PS00665
Dihydrodipicolinate synthase signature 1.
DAPA_THEMA
37-54
4
A:37-54
B:37-54
C:37-54
-
E:37-54
-
2
DHDPS_2
PS00666
Dihydrodipicolinate synthase signature 2.
DAPA_THEMA
132-163
4
A:132-163
B:132-163
C:132-163
-
E:132-163
-
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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
(1, 6)
Info
All SCOP Domains
1a: SCOP_d3pb2a_ (A:)
1b: SCOP_d3pb2b_ (B:)
1c: SCOP_d3pb2c_ (C:)
1d: SCOP_d3pb2d_ (D:)
1e: SCOP_d3pb2e_ (E:)
1f: SCOP_d3pb2f_ (F:)
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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
:
Class I aldolase
(182)
Protein domain
:
automated matches
(54)
Thermotoga maritima [TaxId: 2336]
(3)
1a
d3pb2a_
A:
1b
d3pb2b_
B:
1c
d3pb2c_
C:
1d
d3pb2d_
D:
1e
d3pb2e_
E:
1f
d3pb2f_
F:
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CATH Domains
(0, 0)
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all CATH domains
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Pfam Domains
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Chain C
Chain E
Asymmetric Unit 1
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select chains 'A' and 'C'
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select all 'ALA' residues (Alanines) in chain 'A'
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Show PDB file:
Asym.Unit (313 KB)
Header - Asym.Unit
Biol.Unit 1 (208 KB)
Header - Biol.Unit 1
Biol.Unit 2 (195 KB)
Header - Biol.Unit 2
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