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1RPN
Asym. Unit
Info
Asym.Unit (229 KB)
Biol.Unit 1 (59 KB)
Biol.Unit 2 (59 KB)
Biol.Unit 3 (60 KB)
Biol.Unit 4 (60 KB)
Biol.Unit 5 (221 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF GDP-D-MANNOSE 4,6-DEHYDRATASE IN COMPLEXES WITH GDP AND NADPH
Authors
:
N. A. Webb, A. M. Mulichak, J. S. Lam, H. L. Rocchetta, R. M. Garavito
Date
:
03 Dec 03 (Deposition) - 24 Feb 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.15
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Biol. Unit 5: A,B,C,D (1x)
Keywords
:
Short-Chain Dehydrogenase/Reductase, Rossmann Fold, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
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Reference
:
N. A. Webb, A. M. Mulichak, J. S. Lam, H. L. Rocchetta, R. M. Garavito
Crystal Structure Of A Tetrameric Gdp-D-Mannose 4, 6-Dehydratase From A Bacterial Gdp-D-Rhamnose Biosyntheti Pathway.
Protein Sci. V. 13 529 2004
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Hetero Components
(2, 8)
Info
All Hetero Components
1a: GUANOSINE-5'-DIPHOSPHATE (GDPa)
1b: GUANOSINE-5'-DIPHOSPHATE (GDPb)
1c: GUANOSINE-5'-DIPHOSPHATE (GDPc)
1d: GUANOSINE-5'-DIPHOSPHATE (GDPd)
2a: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPa)
2b: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPb)
2c: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPc)
2d: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPd)
View:
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Label:
No.
Name
Count
Type
Full Name
1
GDP
4
Ligand/Ion
GUANOSINE-5'-DIPHOSPHATE
2
NDP
4
Ligand/Ion
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
[
close Hetero Component info
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Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLY A:9 , THR A:11 , GLY A:12 , GLN A:13 , ASP A:14 , ALA A:34 , ARG A:36 , ASP A:59 , MET A:60 , LEU A:81 , ALA A:82 , ALA A:83 , SER A:85 , VAL A:100 , ALA A:124 , SER A:125 , THR A:126 , TYR A:150 , LYS A:154 , LEU A:177 , ASN A:179 , HIS A:180 , ARG A:185 , HOH A:1604 , HOH A:1609 , HOH A:1613 , HOH A:1617 , HOH A:1618 , HOH A:1620 , HOH A:1622 , HOH A:1637 , HOH A:1641 , HOH A:1650 , HOH A:1660 , HOH A:1673 , HOH A:1698 , HOH A:1723 , ARG D:35 , ARG D:36 , SER D:37
BINDING SITE FOR RESIDUE NDP A 1501
2
AC2
SOFTWARE
GLY B:9 , THR B:11 , GLY B:12 , GLN B:13 , ASP B:14 , ALA B:34 , ARG B:36 , ASP B:59 , MET B:60 , LEU B:81 , ALA B:82 , ALA B:83 , SER B:85 , VAL B:100 , ALA B:124 , SER B:125 , THR B:126 , TYR B:150 , LYS B:154 , LEU B:177 , ASN B:179 , HIS B:180 , ARG B:185 , HOH B:1609 , HOH B:1611 , HOH B:1615 , HOH B:1620 , HOH B:1622 , HOH B:1624 , HOH B:1630 , HOH B:1640 , HOH B:1641 , HOH B:1654 , HOH B:1663 , HOH B:1687 , HOH B:1694 , ARG C:35 , ARG C:36 , SER C:37
BINDING SITE FOR RESIDUE NDP B 1502
3
AC3
SOFTWARE
ARG B:35 , ARG B:36 , SER B:37 , GLY C:9 , THR C:11 , GLY C:12 , GLN C:13 , ASP C:14 , ALA C:34 , ARG C:36 , ASP C:59 , MET C:60 , LEU C:81 , ALA C:82 , ALA C:83 , SER C:85 , VAL C:100 , ALA C:124 , SER C:125 , THR C:126 , TYR C:150 , LYS C:154 , LEU C:177 , ASN C:179 , HIS C:180 , ARG C:185 , HOH C:1613 , HOH C:1615 , HOH C:1622 , HOH C:1623 , HOH C:1624 , HOH C:1632 , HOH C:1634 , HOH C:1643 , HOH C:1644 , HOH C:1648 , HOH C:1664 , HOH C:1696 , HOH C:1702 , HOH C:1717 , HOH C:1729
BINDING SITE FOR RESIDUE NDP C 1503
4
AC4
SOFTWARE
ARG A:35 , ARG A:36 , SER A:37 , HOH A:1682 , GLY D:9 , THR D:11 , GLY D:12 , GLN D:13 , ASP D:14 , ALA D:34 , ARG D:36 , ASP D:59 , MET D:60 , LEU D:81 , ALA D:82 , ALA D:83 , SER D:85 , VAL D:100 , ALA D:124 , SER D:125 , THR D:126 , TYR D:150 , LYS D:154 , LEU D:177 , ASN D:179 , HIS D:180 , ARG D:185 , HOH D:1614 , HOH D:1617 , HOH D:1619 , HOH D:1624 , HOH D:1626 , HOH D:1635 , HOH D:1637 , HOH D:1647 , HOH D:1681 , HOH D:1684 , HOH D:1694 , HOH D:1717
BINDING SITE FOR RESIDUE NDP D 1504
5
AC5
SOFTWARE
PHE A:86 , VAL A:87 , GLU A:128 , ASN A:179 , GLU A:188 , PHE A:189 , VAL A:190 , LYS A:193 , LEU A:211 , GLY A:212 , ASN A:213 , ALA A:216 , ARG A:218 , VAL A:252 , PHE A:277 , ARG A:279 , GLU A:282 , VAL A:283 , HOH A:1615 , HOH A:1616 , HOH A:1633 , HOH A:1638 , HOH A:1670 , HOH A:1679 , HOH A:1723
BINDING SITE FOR RESIDUE GDP A 1601
6
AC6
SOFTWARE
PHE B:86 , VAL B:87 , GLU B:128 , ASN B:179 , GLU B:188 , PHE B:189 , VAL B:190 , LYS B:193 , LEU B:211 , GLY B:212 , ASN B:213 , ALA B:216 , ARG B:218 , VAL B:252 , PHE B:277 , ARG B:279 , GLU B:282 , HOH B:1608 , HOH B:1635 , HOH B:1643 , HOH B:1647 , HOH B:1657 , HOH B:1664
BINDING SITE FOR RESIDUE GDP B 1602
7
AC7
SOFTWARE
PHE C:86 , VAL C:87 , GLU C:128 , ASN C:179 , GLU C:188 , PHE C:189 , VAL C:190 , LYS C:193 , LEU C:211 , GLY C:212 , ASN C:213 , ALA C:216 , ARG C:218 , VAL C:252 , PHE C:277 , ARG C:279 , GLU C:282 , HOH C:1608 , HOH C:1614 , HOH C:1635 , HOH C:1640 , HOH C:1646 , HOH C:1693
BINDING SITE FOR RESIDUE GDP C 1603
8
AC8
SOFTWARE
PHE D:86 , GLU D:128 , ASN D:179 , GLU D:188 , PHE D:189 , VAL D:190 , LYS D:193 , LEU D:211 , GLY D:212 , ASN D:213 , ALA D:216 , ARG D:218 , VAL D:252 , PHE D:277 , ARG D:279 , GLU D:282 , HOH D:1611 , HOH D:1612 , HOH D:1652 , HOH D:1655 , HOH D:1678 , HOH D:1679
BINDING SITE FOR RESIDUE GDP D 1604
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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
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1rpna_ (A:)
1b: SCOP_d1rpnb_ (B:)
1c: SCOP_d1rpnc_ (C:)
1d: SCOP_d1rpnd_ (D:)
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Protein Domains
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(
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Organisms
(
)
(
)
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
:
Tyrosine-dependent oxidoreductases
(503)
Protein domain
:
GDP-mannose 4,6-dehydratase
(5)
Pseudomonas aeruginosa [TaxId: 287]
(1)
1a
d1rpna_
A:
1b
d1rpnb_
B:
1c
d1rpnc_
C:
1d
d1rpnd_
D:
[
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1rpnA01 (A:3-185,A:220-248,A:286-302)
1b: CATH_1rpnB01 (B:3-185,B:220-248,B:286-302)
1c: CATH_1rpnC01 (C:2-185,C:220-248,C:286-302)
1d: CATH_1rpnD01 (D:2-185,D:220-248,D:286-302)
2a: CATH_1rpnA02 (A:186-219,A:249-285,A:303-323)
2b: CATH_1rpnB02 (B:186-219,B:249-285,B:303-323)
2c: CATH_1rpnC02 (C:186-219,C:249-285,C:303-323)
2d: CATH_1rpnD02 (D:186-219,D:249-285,D:303-323)
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Organisms
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(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Pseudomonas aeruginosa. Organism_taxid: 287.
(5)
1a
1rpnA01
A:3-185,A:220-248,A:286-302
1b
1rpnB01
B:3-185,B:220-248,B:286-302
1c
1rpnC01
C:2-185,C:220-248,C:286-302
1d
1rpnD01
D:2-185,D:220-248,D:286-302
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
UDP-galactose 4-epimerase; domain 1
(99)
Homologous Superfamily
:
UDP-galactose 4-epimerase, domain 1
(99)
Pseudomonas aeruginosa. Organism_taxid: 287.
(1)
2a
1rpnA02
A:186-219,A:249-285,A:303-323
2b
1rpnB02
B:186-219,B:249-285,B:303-323
2c
1rpnC02
C:186-219,C:249-285,C:303-323
2d
1rpnD02
D:186-219,D:249-285,D:303-323
[
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Epimerase_1rpnD01 (D:5-245)
1b: PFAM_Epimerase_1rpnD02 (D:5-245)
1c: PFAM_Epimerase_1rpnD03 (D:5-245)
1d: PFAM_Epimerase_1rpnD04 (D:5-245)
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Clan
:
NADP_Rossmann
(1239)
Family
:
Epimerase
(42)
Pseudomonas aeruginosa
(2)
1a
Epimerase-1rpnD01
D:5-245
1b
Epimerase-1rpnD02
D:5-245
1c
Epimerase-1rpnD03
D:5-245
1d
Epimerase-1rpnD04
D:5-245
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Asym.Unit (229 KB)
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