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1NYT
Asym. Unit
Info
Asym.Unit (409 KB)
Biol.Unit 1 (400 KB)
Biol.Unit 2 (796 KB)
Biol.Unit 3 (794 KB)
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(1)
Title
:
SHIKIMATE DEHYDROGENASE AROE COMPLEXED WITH NADP+
Authors
:
A. W. Roszak, A. J. Lapthorn
Date
:
13 Feb 03 (Deposition) - 04 Mar 03 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.50
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: A,B,C,D (2x)
Biol. Unit 3: A,B,C,D (2x)
Keywords
:
Alpha/Beta Domains, Wide Cleft Separation, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. Michel, A. W. Roszak, V. Sauve, J. Maclean, A. Matte, J. R. Coggins, M. Cygler, A. J. Lapthorn
Structures Of Shikimate Dehydrogenase Aroe And Its Paralog Ydib. A Common Structural Framework For Different Activities.
J. Biol. Chem. V. 278 19463 2003
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close entry info
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Hetero Components
(3, 19)
Info
All Hetero Components
1a: (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-D... (DTVa)
2a: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPa)
2b: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPb)
2c: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPc)
2d: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPd)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DTV
1
Ligand/Ion
(2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
2
NAP
4
Ligand/Ion
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
3
SO4
14
Ligand/Ion
SULFATE ION
[
close Hetero Component info
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Sites
(19, 19)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:117 , TYR A:209 , HOH A:1425 , HOH A:1528 , HOH A:1565 , HOH A:1715 , HOH A:1733 , HOH A:1750
BINDING SITE FOR RESIDUE SO4 A 1402
02
AC2
SOFTWARE
HIS A:205 , PRO A:206 , GLY A:207 , HOH A:1437 , HOH A:1577 , HOH A:1769 , HOH A:1789
BINDING SITE FOR RESIDUE SO4 A 1403
03
AC3
SOFTWARE
SER A:14 , SER A:16 , THR A:61 , TYR A:215 , LEU A:241 , DTV A:1405 , HOH A:1681 , HOH A:1724 , HOH A:1725 , HOH A:1726
BINDING SITE FOR RESIDUE SO4 A 1404
04
AC4
SOFTWARE
ARG B:117 , TYR B:209 , HOH B:1435 , HOH B:1580 , HOH B:1715 , HOH B:1752
BINDING SITE FOR RESIDUE SO4 B 1412
05
AC5
SOFTWARE
HIS B:205 , PRO B:206 , GLY B:207 , HOH B:1464 , HOH B:1487 , HOH B:1659 , HOH B:1714 , HOH B:1824
BINDING SITE FOR RESIDUE SO4 B 1413
06
AC6
SOFTWARE
SER B:14 , SER B:16 , THR B:61 , LEU B:241 , HOH B:1482 , HOH B:1566 , HOH B:1769 , HOH B:1770 , HOH B:1774 , HOH B:1775
BINDING SITE FOR RESIDUE SO4 B 1414
07
AC7
SOFTWARE
GLN B:21 , ARG C:117 , HOH C:1551 , HOH C:1578 , HOH C:1656 , HOH C:1675 , HOH C:1678
BINDING SITE FOR RESIDUE SO4 C 1422
08
AC8
SOFTWARE
THR C:61 , LYS C:65 , HOH C:1613
BINDING SITE FOR RESIDUE SO4 C 1423
09
AC9
SOFTWARE
GLU A:111 , SER A:114 , HOH A:1547 , HOH A:1648 , HOH A:1677 , HOH A:1769 , GLN C:26
BINDING SITE FOR RESIDUE SO4 A 1424
10
BC1
SOFTWARE
THR C:61 , VAL C:62 , PRO C:63 , PHE C:64 , LYS C:65 , GLU C:66 , HOH C:1542 , HOH C:1636 , HOH C:1684
BINDING SITE FOR RESIDUE SO4 C 1425
11
BC2
SOFTWARE
PHE C:51 , ARG C:90 , GLY C:94 , HOH C:1526 , HOH C:1655 , ARG D:90 , GLY D:94 , HOH D:1585
BINDING SITE FOR RESIDUE SO4 C 1426
12
BC3
SOFTWARE
ARG D:117 , HOH D:1502 , HOH D:1677
BINDING SITE FOR RESIDUE SO4 D 1432
13
BC4
SOFTWARE
THR D:61 , VAL D:62 , LYS D:65 , NAP D:1431 , HOH D:1581 , HOH D:1597 , HOH D:1613 , HOH D:1673 , HOH D:1678
BINDING SITE FOR RESIDUE SO4 D 1433
14
BC5
SOFTWARE
GLU B:111 , HOH B:1605 , HOH B:1756 , GLN D:26 , HOH D:1686
BINDING SITE FOR RESIDUE SO4 B 1434
15
BC6
SOFTWARE
VAL A:62 , LYS A:65 , ASP A:102 , GLY A:126 , ALA A:127 , GLY A:128 , GLY A:129 , ALA A:130 , ASN A:149 , ARG A:150 , THR A:151 , ARG A:154 , ALA A:187 , THR A:188 , SER A:189 , SER A:190 , MET A:213 , GLY A:237 , MET A:240 , LEU A:241 , DTV A:1405 , HOH A:1432 , HOH A:1440 , HOH A:1448 , HOH A:1453 , HOH A:1474 , HOH A:1494 , HOH A:1495 , HOH A:1578 , HOH A:1599 , HOH A:1622 , HOH A:1623 , HOH A:1665 , HOH A:1722
BINDING SITE FOR RESIDUE NAP A 1401
16
BC7
SOFTWARE
ASN A:59 , VAL A:60 , THR A:61 , VAL A:62 , LYS A:65 , ASN A:86 , ASP A:102 , LEU A:241 , GLN A:244 , NAP A:1401 , SO4 A:1404
BINDING SITE FOR RESIDUE DTV A 1405
17
BC8
SOFTWARE
VAL B:62 , PRO B:63 , LYS B:65 , ASP B:102 , GLY B:126 , ALA B:127 , GLY B:128 , GLY B:129 , ALA B:130 , ASN B:149 , ARG B:150 , THR B:151 , ARG B:154 , ALA B:187 , THR B:188 , SER B:189 , SER B:190 , MET B:213 , GLY B:237 , MET B:240 , LEU B:241 , HOH B:1444 , HOH B:1465 , HOH B:1468 , HOH B:1481 , HOH B:1490 , HOH B:1500 , HOH B:1513 , HOH B:1531 , HOH B:1548 , HOH B:1603 , HOH B:1616 , HOH B:1720 , HOH B:1741 , HOH B:1773
BINDING SITE FOR RESIDUE NAP B 1411
18
BC9
SOFTWARE
GLY C:126 , ALA C:127 , GLY C:128 , GLY C:129 , ALA C:130 , ASN C:149 , ARG C:150 , THR C:151 , ARG C:154 , ALA C:187 , THR C:188 , SER C:189 , MET C:213 , GLY C:237 , MET C:240 , LEU C:241 , GLN C:244 , HOH C:1515 , HOH C:1540 , HOH C:1555 , HOH C:1602 , HOH C:1616 , HOH C:1634
BINDING SITE FOR RESIDUE NAP C 1421
19
CC1
SOFTWARE
VAL D:62 , ASP D:102 , GLY D:126 , ALA D:127 , GLY D:128 , GLY D:129 , ALA D:130 , ASN D:149 , ARG D:150 , THR D:151 , ARG D:154 , ALA D:187 , THR D:188 , SER D:189 , SER D:190 , MET D:213 , TYR D:215 , GLY D:237 , MET D:240 , LEU D:241 , SO4 D:1433 , HOH D:1455 , HOH D:1468 , HOH D:1503 , HOH D:1538 , HOH D:1545 , HOH D:1568 , HOH D:1581 , HOH D:1610 , HOH D:1613 , HOH D:1642 , HOH D:1646 , HOH D:1703
BINDING SITE FOR RESIDUE NAP D 1431
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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Sorry, no Info available
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Exons
(0, 0)
Info
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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
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1nyta2 (A:1-101)
1b: SCOP_d1nytb2 (B:1-101)
1c: SCOP_d1nytc2 (C:1-101)
1d: SCOP_d1nytd2 (D:1-101)
2a: SCOP_d1nyta1 (A:102-271)
2b: SCOP_d1nytb1 (B:102-271)
2c: SCOP_d1nytc1 (C:102-269)
2d: SCOP_d1nytd1 (D:102-270)
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)
(
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Aminoacid dehydrogenase-like, N-terminal domain
(100)
Superfamily
:
Aminoacid dehydrogenase-like, N-terminal domain
(100)
Family
:
Shikimate dehydrogenase-like
(14)
Protein domain
:
Shikimate 5-dehydrogenase AroE
(10)
Escherichia coli [TaxId: 562]
(1)
1a
d1nyta2
A:1-101
1b
d1nytb2
B:1-101
1c
d1nytc2
C:1-101
1d
d1nytd2
D:1-101
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
Aminoacid dehydrogenase-like, C-terminal domain
(67)
Protein domain
:
Shikimate 5-dehydrogenase AroE
(10)
Escherichia coli [TaxId: 562]
(1)
2a
d1nyta1
A:102-271
2b
d1nytb1
B:102-271
2c
d1nytc1
C:102-269
2d
d1nytd1
D:102-270
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1nytA01 (A:1-101,A:245-258)
1b: CATH_1nytB01 (B:1-101,B:245-258)
1c: CATH_1nytC01 (C:1-101,C:245-258)
1d: CATH_1nytD01 (D:1-101,D:245-258)
2a: CATH_1nytA02 (A:102-244)
2b: CATH_1nytB02 (B:102-244)
2c: CATH_1nytC02 (C:102-244)
2d: CATH_1nytD02 (D:102-244)
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Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Leucine Dehydrogenase; Chain A, domain 1
(52)
Homologous Superfamily
:
Leucine Dehydrogenase, chain A, domain 1
(52)
Escherichia coli. Organism_taxid: 562.
(2)
1a
1nytA01
A:1-101,A:245-258
1b
1nytB01
B:1-101,B:245-258
1c
1nytC01
C:1-101,C:245-258
1d
1nytD01
D:1-101,D:245-258
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Escherichia coli. Organism_taxid: 562.
(48)
2a
1nytA02
A:102-244
2b
1nytB02
B:102-244
2c
1nytC02
C:102-244
2d
1nytD02
D:102-244
[
close CATH info
]
Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_Shikimate_DH_1nytD01 (D:111-213)
1b: PFAM_Shikimate_DH_1nytD02 (D:111-213)
1c: PFAM_Shikimate_DH_1nytD03 (D:111-213)
1d: PFAM_Shikimate_DH_1nytD04 (D:111-213)
2a: PFAM_Shikimate_dh_N_1nytD05 (D:6-88)
2b: PFAM_Shikimate_dh_N_1nytD06 (D:6-88)
2c: PFAM_Shikimate_dh_N_1nytD07 (D:6-88)
2d: PFAM_Shikimate_dh_N_1nytD08 (D:6-88)
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Clans
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(
)
Organisms
(
)
(
)
Clan
:
NADP_Rossmann
(1239)
Family
:
Shikimate_DH
(16)
Escherichia coli (strain K12)
(3)
1a
Shikimate_DH-1nytD01
D:111-213
1b
Shikimate_DH-1nytD02
D:111-213
1c
Shikimate_DH-1nytD03
D:111-213
1d
Shikimate_DH-1nytD04
D:111-213
Clan
:
no clan defined [family: Shikimate_dh_N]
(15)
Family
:
Shikimate_dh_N
(15)
Escherichia coli (strain K12)
(3)
2a
Shikimate_dh_N-1nytD05
D:6-88
2b
Shikimate_dh_N-1nytD06
D:6-88
2c
Shikimate_dh_N-1nytD07
D:6-88
2d
Shikimate_dh_N-1nytD08
D:6-88
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