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1MUU
Asym. Unit
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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
(4, 45)
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
4
Ligand/Ion
GUANOSINE 5'-(TRIHYDROGEN DIPHOSPHATE), P'-D-MANNOPYRANOSYL ESTER
2
MSE
36
Mod. Amino Acid
SELENOMETHIONINE
3
NAD
4
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
4
SUC
1
Ligand/Ion
SUCROSE
[
close Hetero Component info
]
Sites
(9, 9)
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)
9: AC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LYS C:315 , ALA C:389 , SER C:391 , ASP C:392 , SER C:412 , GLY C:413 , LYS C:414 , HOH C:1215 , HOH C:1232 , LYS D:366
BINDING SITE FOR RESIDUE SUC C 1009
2
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
3
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
4
AC4
SOFTWARE
GLY C:7 , GLY C:9 , TYR C:10 , VAL C:11 , VAL C:29 , ASP C:30 , VAL C:31 , LYS C:35 , CYS C:83 , VAL C:84 , GLY C:85 , THR C:86 , THR C:101 , VAL C:102 , GLU C:105 , SER C:123 , THR C:124 , GLU C:157 , HOH C:1024 , HOH C:1048 , HOH C:1070 , HOH C:1073 , HOH C:1103 , HOH C:1126 , HOH C:1250 , LYS D:271 , ARG D:331
BINDING SITE FOR RESIDUE NAD C 1003
5
AC5
SOFTWARE
LYS C:271 , ARG C:331 , GLY D:7 , GLY D:9 , TYR D:10 , VAL D:11 , VAL D:29 , ASP D:30 , LYS D:35 , CYS D:83 , VAL D:84 , GLY D:85 , THR D:86 , TYR D:98 , THR D:101 , VAL D:102 , GLU D:105 , SER D:123 , THR D:124 , GLU D:157 , HOH D:1024 , HOH D:1054 , HOH D:1056 , HOH D:1070 , HOH D:1079 , HOH D:1086 , HOH D:1127 , HOH D:1251
BINDING SITE FOR RESIDUE NAD D 1004
6
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
7
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
8
AC8
SOFTWARE
GLU C:157 , PHE C:158 , LEU C:159 , ARG C:160 , GLU C:161 , LYS C:210 , ASN C:214 , HIS C:217 , VAL C:221 , ASN C:225 , HOH C:1024 , TYR D:256 , TYR D:257 , MSE D:258 , ARG D:259 , PHE D:262 , PHE D:264 , GLY D:265 , CYS D:268 , LEU D:269 , PHE D:323 , LYS D:324 , HOH D:1038 , HOH D:1048 , HOH D:1065 , HOH D:1130
BINDING SITE FOR RESIDUE GDX D 1007
9
AC9
SOFTWARE
TYR C:256 , TYR C:257 , MSE C:258 , ARG C:259 , PHE C:262 , PHE C:264 , GLY C:265 , CYS C:268 , PHE C:323 , LYS C:324 , HOH C:1139 , GLU D:157 , PHE D:158 , LEU D:159 , ARG D:160 , GLU D:161 , LYS D:210 , ASN D:214 , HIS D:217 , VAL D:221 , ASN D:225 , HOH D:1024 , HOH D:1059 , HOH D:1073 , HOH D:1085 , HOH D:1089
BINDING SITE FOR RESIDUE GDX D 1008
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
[
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]
Exons
(0, 0)
Info
All Exons
View:
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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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Classes
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)
(
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Folds
(
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(
)
Superfamilies
(
)
(
)
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)
View:
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)
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Architectures
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)
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)
Topologies
(
)
(
)
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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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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