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1VM6
Asym. Unit
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Asym.Unit (161 KB)
Biol.Unit 1 (151 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF DIHYDRODIPICOLINATE REDUCTASE (TM1520) FROM THERMOTOGA MARITIMA AT 2.27 A RESOLUTION
Authors
:
Joint Center For Structural Genomics (Jcsg)
Date
:
03 Sep 04 (Deposition) - 21 Sep 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.27
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Tm1520, Dihydrodipicolinate Reductase, Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Joint Center For Structural Genomics, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Dihydrodipicolinate Reductase (Tm1520) From Thermotoga Maritima At 2. 27 A Resolution
To Be Published
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Hetero Components
(4, 21)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
1c: ACETATE ION (ACTc)
1d: ACETATE ION (ACTd)
1e: ACETATE ION (ACTe)
1f: ACETATE ION (ACTf)
1g: ACETATE ION (ACTg)
1h: ACETATE ION (ACTh)
1i: ACETATE ION (ACTi)
1j: ACETATE ION (ACTj)
1k: ACETATE ION (ACTk)
1l: ACETATE ION (ACTl)
2a: 1,2-ETHANEDIOL (EDOa)
3a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
3b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
3c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
3d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
4a: TETRAETHYLENE GLYCOL (PG4a)
4b: TETRAETHYLENE GLYCOL (PG4b)
4c: TETRAETHYLENE GLYCOL (PG4c)
4d: TETRAETHYLENE GLYCOL (PG4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
12
Ligand/Ion
ACETATE ION
2
EDO
1
Ligand/Ion
1,2-ETHANEDIOL
3
NAD
4
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
4
PG4
4
Ligand/Ion
TETRAETHYLENE GLYCOL
[
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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
SER B:183 , ARG B:184
BINDING SITE FOR RESIDUE ACT B 217
02
AC2
SOFTWARE
HIS B:127 , HIS B:128 , LYS B:131 , ACT B:222 , NAD B:300 , HOH B:315 , HOH B:317 , HOH B:342
BINDING SITE FOR RESIDUE ACT B 218
03
AC3
SOFTWARE
ASP C:43 , GLY C:67 , GLY C:200
BINDING SITE FOR RESIDUE ACT C 217
04
AC4
SOFTWARE
GLU B:176
BINDING SITE FOR RESIDUE ACT B 219
05
AC5
SOFTWARE
HIS A:127 , HIS A:128 , LYS A:131 , ACT A:218 , NAD A:300 , HOH A:318 , HOH A:326 , HOH A:392
BINDING SITE FOR RESIDUE ACT A 217
06
AC6
SOFTWARE
SER B:110 , LYS B:114 , ALA B:145
BINDING SITE FOR RESIDUE ACT B 220
07
AC7
SOFTWARE
PHE B:98 , ILE B:100 , VAL B:186 , GLY B:190 , LYS B:193 , HOH C:309
BINDING SITE FOR RESIDUE ACT B 221
08
AC8
SOFTWARE
PHE B:108 , LEU B:112 , PHE C:108 , GLU C:111
BINDING SITE FOR RESIDUE ACT C 218
09
AC9
SOFTWARE
THR D:73 , ASP D:133 , NAD D:300 , HOH D:321 , HOH D:382
BINDING SITE FOR RESIDUE ACT D 217
10
BC1
SOFTWARE
THR A:73 , TYR A:96 , LYS A:131 , SER A:136 , GLY A:137 , THR A:138 , ACT A:217 , NAD A:300
BINDING SITE FOR RESIDUE ACT A 218
11
BC2
SOFTWARE
THR D:73 , TYR D:96 , LYS D:131 , SER D:136 , GLY D:137 , THR D:138
BINDING SITE FOR RESIDUE ACT D 218
12
BC3
SOFTWARE
THR B:73 , TYR B:96 , LYS B:131 , SER B:136 , GLY B:137 , THR B:138 , ACT B:218 , NAD B:300
BINDING SITE FOR RESIDUE ACT B 222
13
BC4
SOFTWARE
GLY A:7 , SER A:9 , GLY A:10 , ARG A:11 , MET A:12 , ASP A:32 , VAL A:33 , PHE A:48 , SER A:49 , SER A:50 , ALA A:53 , GLY A:71 , THR A:73 , ALA A:95 , TYR A:96 , ASN A:97 , PHE A:98 , LYS A:131 , PHE A:187 , ACT A:217 , ACT A:218 , HOH A:313 , HOH A:314 , HOH A:318 , HOH A:326
BINDING SITE FOR RESIDUE NAD A 300
14
BC5
SOFTWARE
GLY B:7 , SER B:9 , GLY B:10 , ARG B:11 , MET B:12 , ASP B:32 , VAL B:33 , PHE B:48 , SER B:49 , SER B:50 , GLU B:52 , ALA B:53 , GLY B:71 , THR B:73 , ALA B:95 , TYR B:96 , ASN B:97 , PHE B:98 , LYS B:131 , ASP B:133 , PHE B:187 , ACT B:218 , ACT B:222 , HOH B:307 , HOH B:315 , HOH B:316 , HOH B:338 , HOH B:342 , HOH B:387 , HOH B:435 , HOH B:485
BINDING SITE FOR RESIDUE NAD B 300
15
BC6
SOFTWARE
GLY C:7 , SER C:9 , GLY C:10 , ARG C:11 , MET C:12 , ASP C:32 , VAL C:33 , PHE C:48 , SER C:49 , SER C:50 , GLU C:52 , ALA C:53 , GLY C:71 , THR C:72 , THR C:73 , ALA C:95 , TYR C:96 , ASN C:97 , PHE C:98 , PHE C:187 , PG4 C:302 , HOH C:337 , HOH C:342 , HOH C:384
BINDING SITE FOR RESIDUE NAD C 300
16
BC7
SOFTWARE
GLY D:7 , SER D:9 , GLY D:10 , ARG D:11 , MET D:12 , ASP D:32 , VAL D:33 , PHE D:48 , SER D:49 , SER D:50 , ALA D:53 , GLY D:71 , THR D:72 , THR D:73 , ALA D:95 , TYR D:96 , ASN D:97 , PHE D:98 , LYS D:131 , ASP D:133 , PHE D:187 , ACT D:217 , HOH D:319 , HOH D:325 , HOH D:331 , HOH D:367 , HOH D:395 , HOH D:431
BINDING SITE FOR RESIDUE NAD D 300
17
BC8
SOFTWARE
HIS B:-1 , HIS B:-2 , MET B:1 , ASP B:43 , HOH B:355 , HOH B:436 , ARG C:84 , SER C:87 , GLY C:204 , MET C:205
BINDING SITE FOR RESIDUE EDO C 301
18
BC9
SOFTWARE
TYR C:96 , PRO C:161 , SER C:183 , ARG C:184 , NAD C:300 , HOH C:326
BINDING SITE FOR RESIDUE PG4 C 302
19
CC1
SOFTWARE
TYR B:8 , GLN B:17 , LYS B:30 , GLU B:37 , LEU B:39
BINDING SITE FOR RESIDUE PG4 B 301
20
CC2
SOFTWARE
LEU B:75 , LEU B:80 , TYR B:96 , HOH B:492 , HOH B:493
BINDING SITE FOR RESIDUE PG4 B 302
21
CC3
SOFTWARE
ARG B:107 , PHE B:108 , PHE B:213
BINDING SITE FOR RESIDUE PG4 B 303
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Select:
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Sorry, no Info available
[
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: DAPB (A:122-139,B:122-139,C:122-139,D:12...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DAPB
PS01298
Dihydrodipicolinate reductase signature.
DAPB_THEMA
122-139
4
A:122-139
B:122-139
C:122-139
D:122-139
[
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Exons
(0, 0)
Info
All Exons
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Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1vm6a2 (A:97-182)
1b: SCOP_d1vm6b2 (B:97-182)
1c: SCOP_d1vm6c2 (C:97-182)
1d: SCOP_d1vm6d2 (D:97-182)
2a: SCOP_d1vm6a3 (A:1-96,A:183-214)
2b: SCOP_d1vm6b1 (B:1-96,B:183-213)
2c: SCOP_d1vm6c3 (C:1-96,C:183-214)
2d: SCOP_d1vm6d1 (D:1-96,D:183-213)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
FwdE/GAPDH domain-like
(188)
Superfamily
:
Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
(179)
Family
:
Dihydrodipicolinate reductase-like
(45)
Protein domain
:
Dihydrodipicolinate reductase
(11)
Thermotoga maritima [TaxId: 2336]
(1)
1a
d1vm6a2
A:97-182
1b
d1vm6b2
B:97-182
1c
d1vm6c2
C:97-182
1d
d1vm6d2
D:97-182
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
(179)
Protein domain
:
Dihydrodipicolinate reductase
(11)
Thermotoga maritima [TaxId: 2336]
(1)
2a
d1vm6a3
A:1-96,A:183-214
2b
d1vm6b1
B:1-96,B:183-213
2c
d1vm6c3
C:1-96,C:183-214
2d
d1vm6d1
D:1-96,D:183-213
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1vm6A02 (A:100-182)
1b: CATH_1vm6D02 (D:100-182)
1c: CATH_1vm6B02 (B:100-182)
1d: CATH_1vm6C02 (C:100-182)
2a: CATH_1vm6B01 (B:-4-99,B:183-213)
2b: CATH_1vm6D01 (D:-3-99,D:183-213)
2c: CATH_1vm6A01 (A:0-99,A:183-214)
2d: CATH_1vm6C01 (C:1-99,C:183-215)
View:
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Classes
(
)
(
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Architectures
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Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Dihydrodipicolinate Reductase; domain 2
(182)
Homologous Superfamily
:
Dihydrodipicolinate Reductase; domain 2
(178)
Thermotoga maritima. Organism_taxid: 2336.
(4)
1a
1vm6A02
A:100-182
1b
1vm6D02
D:100-182
1c
1vm6B02
B:100-182
1d
1vm6C02
C:100-182
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Thermotoga maritima. Organism_taxid: 2336.
(10)
2a
1vm6B01
B:-4-99,B:183-213
2b
1vm6D01
D:-3-99,D:183-213
2c
1vm6A01
A:0-99,A:183-214
2d
1vm6C01
C:1-99,C:183-215
[
close CATH info
]
Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_DapB_N_1vm6D01 (D:1-98)
1b: PFAM_DapB_N_1vm6D02 (D:1-98)
1c: PFAM_DapB_N_1vm6D03 (D:1-98)
1d: PFAM_DapB_N_1vm6D04 (D:1-98)
2a: PFAM_DapB_C_1vm6D05 (D:101-212)
2b: PFAM_DapB_C_1vm6D06 (D:101-212)
2c: PFAM_DapB_C_1vm6D07 (D:101-212)
2d: PFAM_DapB_C_1vm6D08 (D:101-212)
View:
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Clans
(
)
(
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Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
NADP_Rossmann
(1239)
Family
:
DapB_N
(5)
Thermotoga maritima
(1)
1a
DapB_N-1vm6D01
D:1-98
1b
DapB_N-1vm6D02
D:1-98
1c
DapB_N-1vm6D03
D:1-98
1d
DapB_N-1vm6D04
D:1-98
Clan
:
no clan defined [family: DapB_C]
(5)
Family
:
DapB_C
(5)
Thermotoga maritima
(1)
2a
DapB_C-1vm6D05
D:101-212
2b
DapB_C-1vm6D06
D:101-212
2c
DapB_C-1vm6D07
D:101-212
2d
DapB_C-1vm6D08
D:101-212
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