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1MUU
Biol. Unit 1
Info
Asym.Unit (292 KB)
Biol.Unit 1 (142 KB)
Biol.Unit 2 (145 KB)
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(1)
Title
:
2.0 A CRYSTAL STRUCTURE OF GDP-MANNOSE DEHYDROGENASE
Authors
:
C. F. Snook, P. A. Tipton, L. J. Beamer
Date
:
24 Sep 02 (Deposition) - 06 May 03 (Release) - 12 Nov 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.02
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Rossmann Fold; Domain-Swapped Dimer; Enzyme Complex With Cofactor And Product, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. F. Snook, P. A. Tipton, L. J. Beamer
Crystal Structure Of Gdp-Mannose Dehydrogenase: A Key Enzym Of Alginate Biosynthesis In P. Aeruginosa
Biochemistry V. 42 4658 2003
(for further references see the
PDB file header
)
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Hetero Components
(3, 22)
Info
All Hetero Components
1a: GUANOSINE 5'-(TRIHYDROGEN DIPHOSPH... (GDXa)
1b: GUANOSINE 5'-(TRIHYDROGEN DIPHOSPH... (GDXb)
1c: GUANOSINE 5'-(TRIHYDROGEN DIPHOSPH... (GDXc)
1d: GUANOSINE 5'-(TRIHYDROGEN DIPHOSPH... (GDXd)
2a: SELENOMETHIONINE (MSEa)
2aa: SELENOMETHIONINE (MSEaa)
2ab: SELENOMETHIONINE (MSEab)
2ac: SELENOMETHIONINE (MSEac)
2ad: SELENOMETHIONINE (MSEad)
2ae: SELENOMETHIONINE (MSEae)
2af: SELENOMETHIONINE (MSEaf)
2ag: SELENOMETHIONINE (MSEag)
2ah: SELENOMETHIONINE (MSEah)
2ai: SELENOMETHIONINE (MSEai)
2aj: SELENOMETHIONINE (MSEaj)
2b: SELENOMETHIONINE (MSEb)
2c: SELENOMETHIONINE (MSEc)
2d: SELENOMETHIONINE (MSEd)
2e: SELENOMETHIONINE (MSEe)
2f: SELENOMETHIONINE (MSEf)
2g: SELENOMETHIONINE (MSEg)
2h: SELENOMETHIONINE (MSEh)
2i: SELENOMETHIONINE (MSEi)
2j: SELENOMETHIONINE (MSEj)
2k: SELENOMETHIONINE (MSEk)
2l: SELENOMETHIONINE (MSEl)
2m: SELENOMETHIONINE (MSEm)
2n: SELENOMETHIONINE (MSEn)
2o: SELENOMETHIONINE (MSEo)
2p: SELENOMETHIONINE (MSEp)
2q: SELENOMETHIONINE (MSEq)
2r: SELENOMETHIONINE (MSEr)
2s: SELENOMETHIONINE (MSEs)
2t: SELENOMETHIONINE (MSEt)
2u: SELENOMETHIONINE (MSEu)
2v: SELENOMETHIONINE (MSEv)
2w: SELENOMETHIONINE (MSEw)
2x: SELENOMETHIONINE (MSEx)
2y: SELENOMETHIONINE (MSEy)
2z: SELENOMETHIONINE (MSEz)
3a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
3b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
3c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
3d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
4a: SUCROSE (SUCa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GDX
2
Ligand/Ion
GUANOSINE 5'-(TRIHYDROGEN DIPHOSPHATE), P'-D-MANNOPYRANOSYL ESTER
2
MSE
18
Mod. Amino Acid
SELENOMETHIONINE
3
NAD
2
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
4
SUC
-1
Ligand/Ion
SUCROSE
[
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]
Sites
(4, 4)
Info
All Sites
1: AC2 (SOFTWARE)
2: AC3 (SOFTWARE)
3: AC6 (SOFTWARE)
4: AC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC2
SOFTWARE
GLY A:7 , GLY A:9 , TYR A:10 , VAL A:11 , ASP A:30 , VAL A:31 , LYS A:35 , CYS A:83 , VAL A:84 , GLY A:85 , THR A:86 , TYR A:98 , THR A:101 , VAL A:102 , GLU A:105 , SER A:123 , THR A:124 , GLU A:157 , HOH A:1015 , HOH A:1044 , HOH A:1051 , HOH A:1058 , HOH A:1131 , LYS B:271 , ARG B:331 , HOH B:1116
BINDING SITE FOR RESIDUE NAD A 1001
2
AC3
SOFTWARE
LYS A:271 , ARG A:331 , GLY B:7 , GLY B:9 , TYR B:10 , VAL B:11 , VAL B:29 , ASP B:30 , VAL B:31 , LYS B:35 , CYS B:83 , VAL B:84 , GLY B:85 , THR B:86 , TYR B:98 , THR B:101 , VAL B:102 , GLU B:105 , SER B:123 , THR B:124 , GLU B:157 , HOH B:1014 , HOH B:1036 , HOH B:1083 , HOH B:1110 , HOH B:1113 , HOH B:1191 , HOH B:1215
BINDING SITE FOR RESIDUE NAD B 1002
3
AC6
SOFTWARE
GLU A:157 , PHE A:158 , LEU A:159 , ARG A:160 , GLU A:161 , LYS A:210 , ASN A:214 , HIS A:217 , VAL A:221 , ASN A:225 , TYR B:256 , TYR B:257 , MSE B:258 , ARG B:259 , PHE B:262 , PHE B:264 , GLY B:265 , CYS B:268 , LEU B:269 , PHE B:323 , LYS B:324 , HOH B:1028 , HOH B:1043 , HOH B:1057 , HOH B:1082 , HOH B:1168
BINDING SITE FOR RESIDUE GDX B 1005
4
AC7
SOFTWARE
TYR A:256 , TYR A:257 , MSE A:258 , ARG A:259 , GLY A:261 , PHE A:262 , PHE A:264 , GLY A:265 , CYS A:268 , PHE A:323 , LYS A:324 , HOH A:1017 , GLU B:157 , PHE B:158 , LEU B:159 , ARG B:160 , GLU B:161 , LYS B:210 , ASN B:214 , HIS B:217 , VAL B:221 , ASN B:225 , HOH B:1014 , HOH B:1017 , HOH B:1032 , HOH B:1111 , HOH B:1143
BINDING SITE FOR RESIDUE GDX B 1006
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
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End label:
Sorry, no Info available
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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
(3, 12)
Info
All SCOP Domains
1a: SCOP_d1muua1 (A:203-300)
1b: SCOP_d1muub1 (B:203-300)
1c: SCOP_d1muuc1 (C:203-300)
1d: SCOP_d1muud1 (D:203-300)
2a: SCOP_d1muua3 (A:301-436)
2b: SCOP_d1muub3 (B:301-436)
2c: SCOP_d1muuc3 (C:301-436)
2d: SCOP_d1muud3 (D:301-436)
3a: SCOP_d1muua2 (A:1-202)
3b: SCOP_d1muub2 (B:1-202)
3c: SCOP_d1muuc2 (C:1-202)
3d: SCOP_d1muud2 (D:1-202)
View:
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)
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)
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(
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)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
6-phosphogluconate dehydrogenase C-terminal domain-like
(119)
Superfamily
:
6-phosphogluconate dehydrogenase C-terminal domain-like
(119)
Family
:
UDP-glucose/GDP-mannose dehydrogenase dimerisation domain
(5)
Protein domain
:
GDP-mannose 6-dehydrogenase, middle domain
(3)
Pseudomonas aeruginosa [TaxId: 287]
(3)
1a
d1muua1
A:203-300
1b
d1muub1
B:203-300
1c
d1muuc1
C:203-300
1d
d1muud1
D:203-300
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Adenine nucleotide alpha hydrolase-like
(440)
Superfamily
:
UDP-glucose/GDP-mannose dehydrogenase C-terminal domain
(5)
Family
:
UDP-glucose/GDP-mannose dehydrogenase C-terminal domain
(5)
Protein domain
:
GDP-mannose 6-dehydrogenase, GDP-binding domain
(3)
Pseudomonas aeruginosa [TaxId: 287]
(3)
2a
d1muua3
A:301-436
2b
d1muub3
B:301-436
2c
d1muuc3
C:301-436
2d
d1muud3
D:301-436
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
6-phosphogluconate dehydrogenase-like, N-terminal domain
(69)
Protein domain
:
GDP-mannose 6-dehydrogenase
(3)
Pseudomonas aeruginosa [TaxId: 287]
(3)
3a
d1muua2
A:1-202
3b
d1muub2
B:1-202
3c
d1muuc2
C:1-202
3d
d1muud2
D:1-202
[
close SCOP info
]
CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_1muuA01 (A:2-202)
1b: CATH_1muuA03 (A:235-436)
1c: CATH_1muuB03 (B:235-436)
1d: CATH_1muuC03 (C:235-436)
1e: CATH_1muuD03 (D:235-436)
1f: CATH_1muuB01 (B:2-202)
1g: CATH_1muuC01 (C:2-202)
1h: CATH_1muuD01 (D:2-202)
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Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
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
1muuA01
A:2-202
1b
1muuA03
A:235-436
1c
1muuB03
B:235-436
1d
1muuC03
C:235-436
1e
1muuD03
D:235-436
1f
1muuB01
B:2-202
1g
1muuC01
C:2-202
1h
1muuD01
D:2-202
[
close CATH info
]
Pfam Domains
(3, 12)
Info
all PFAM domains
1a: PFAM_UDPG_MGDP_dh_1muuD01 (D:203-300)
1b: PFAM_UDPG_MGDP_dh_1muuD02 (D:203-300)
1c: PFAM_UDPG_MGDP_dh_1muuD03 (D:203-300)
1d: PFAM_UDPG_MGDP_dh_1muuD04 (D:203-300)
2a: PFAM_UDPG_MGDP_dh_N_1muuD05 (D:1-190)
2b: PFAM_UDPG_MGDP_dh_N_1muuD06 (D:1-190)
2c: PFAM_UDPG_MGDP_dh_N_1muuD07 (D:1-190)
2d: PFAM_UDPG_MGDP_dh_N_1muuD08 (D:1-190)
3a: PFAM_UDPG_MGDP_dh_C_1muuD09 (D:317-423)
3b: PFAM_UDPG_MGDP_dh_C_1muuD10 (D:317-423)
3c: PFAM_UDPG_MGDP_dh_C_1muuD11 (D:317-423)
3d: PFAM_UDPG_MGDP_dh_C_1muuD12 (D:317-423)
View:
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Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
6PGD_C
(47)
Family
:
UDPG_MGDP_dh
(10)
Pseudomonas aeruginosa
(3)
1a
UDPG_MGDP_dh-1muuD01
D:203-300
1b
UDPG_MGDP_dh-1muuD02
D:203-300
1c
UDPG_MGDP_dh-1muuD03
D:203-300
1d
UDPG_MGDP_dh-1muuD04
D:203-300
Clan
:
NADP_Rossmann
(1239)
Family
:
UDPG_MGDP_dh_N
(10)
Pseudomonas aeruginosa
(3)
2a
UDPG_MGDP_dh_N-1muuD05
D:1-190
2b
UDPG_MGDP_dh_N-1muuD06
D:1-190
2c
UDPG_MGDP_dh_N-1muuD07
D:1-190
2d
UDPG_MGDP_dh_N-1muuD08
D:1-190
Clan
:
no clan defined [family: UDPG_MGDP_dh_C]
(10)
Family
:
UDPG_MGDP_dh_C
(10)
Pseudomonas aeruginosa
(3)
3a
UDPG_MGDP_dh_C-1muuD09
D:317-423
3b
UDPG_MGDP_dh_C-1muuD10
D:317-423
3c
UDPG_MGDP_dh_C-1muuD11
D:317-423
3d
UDPG_MGDP_dh_C-1muuD12
D:317-423
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