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1MV8
Asym. Unit
Info
Asym.Unit (304 KB)
Biol.Unit 1 (148 KB)
Biol.Unit 2 (153 KB)
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(1)
Title
:
1.55 A CRYSTAL STRUCTURE OF A TERNARY COMPLEX OF GDP-MANNOSE DEHYDROGENASE FROM PSUEDOMONAS AERUGINOSA
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
:
1.55
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
The Crystal Structure Of Gdp-Mannose Dehydrogenase: A Key Enzyme In Alginate Biosynthesis Of P. Aeruginosa
Biochemistry V. 42 4658 2003
(for further references see the
PDB file header
)
[
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Hetero Components
(5, 13)
Info
All Hetero Components
1a: ACETIC ACID (ACYa)
1b: ACETIC ACID (ACYb)
2a: GUANOSINE 5'-(TRIHYDROGEN DIPHOSPH... (GDXa)
2b: GUANOSINE 5'-(TRIHYDROGEN DIPHOSPH... (GDXb)
2c: GUANOSINE 5'-(TRIHYDROGEN DIPHOSPH... (GDXc)
2d: GUANOSINE 5'-(TRIHYDROGEN DIPHOSPH... (GDXd)
3a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
4a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
4b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
4c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
4d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
5a: SUCROSE (SUCa)
5b: SUCROSE (SUCb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACY
2
Ligand/Ion
ACETIC ACID
2
GDX
4
Ligand/Ion
GUANOSINE 5'-(TRIHYDROGEN DIPHOSPHATE), P'-D-MANNOPYRANOSYL ESTER
3
MPD
1
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
4
NAD
4
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
5
SUC
2
Ligand/Ion
SUCROSE
[
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Sites
(13, 13)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LYS B:181 , ASP B:185 , HOH B:2190 , HOH B:2297 , ARG C:192 , HOH C:2112 , HOH C:2238 , GLU D:139 , ASP D:140
BINDING SITE FOR RESIDUE SUC B 2012
02
AC2
SOFTWARE
ASP A:195 , PRO A:197 , HOH A:2083 , GLN B:247 , HIS B:249 , HOH B:2159 , LEU D:194 , ASP D:195 , HOH D:2128 , HOH D:2136 , HOH D:2213 , HOH D:2395 , HOH D:2399
BINDING SITE FOR RESIDUE SUC D 2013
03
AC3
SOFTWARE
GLY A:7 , GLY A:9 , TYR A:10 , VAL A:11 , VAL A:29 , ASP A:30 , VAL A:31 , LYS A:35 , CYS A:83 , VAL A:84 , GLY A:85 , THR A:86 , TYR A:98 , VAL A:102 , GLU A:105 , SER A:123 , THR A:124 , GLU A:157 , HOH A:2019 , HOH A:2067 , HOH A:2097 , HOH A:2147 , HOH A:2206 , HOH A:2239 , HOH A:2244 , LYS B:271 , ARG B:331 , HOH B:2143
BINDING SITE FOR RESIDUE NAD A 2001
04
AC4
SOFTWARE
LYS A:271 , ARG A:331 , HOH A:2243 , 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:2037 , HOH B:2079 , HOH B:2101 , HOH B:2129 , HOH B:2140 , HOH B:2227 , HOH B:2229
BINDING SITE FOR RESIDUE NAD B 2002
05
AC5
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 , TYR C:98 , VAL C:102 , GLU C:105 , SER C:123 , THR C:124 , GLU C:157 , HOH C:2047 , HOH C:2068 , HOH C:2071 , HOH C:2100 , HOH C:2120 , HOH C:2227 , HOH C:2284 , HOH C:2370 , HOH C:2393 , LYS D:271 , ARG D:331 , HOH D:2027
BINDING SITE FOR RESIDUE NAD C 2003
06
AC6
SOFTWARE
LYS C:271 , ARG C:331 , HOH C:2051 , GLY D:7 , GLY D:9 , TYR D:10 , VAL D:11 , VAL D:29 , ASP D:30 , VAL D:31 , LYS D:35 , CYS D:83 , VAL D:84 , GLY D:85 , THR D:86 , TYR D:98 , VAL D:102 , GLU D:105 , SER D:123 , THR D:124 , GLU D:157 , HOH D:2014 , HOH D:2059 , HOH D:2070 , HOH D:2123 , HOH D:2206 , HOH D:2341 , HOH D:2342
BINDING SITE FOR RESIDUE NAD D 2004
07
AC7
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 , HOH A:2020 , HOH A:2031 , HOH A:2046 , HOH A:2139 , HOH A:2201 , LEU B:251 , TYR B:256 , TYR B:257 , MET 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:2032 , HOH B:2143
BINDING SITE FOR RESIDUE GDX A 2005
08
AC8
SOFTWARE
TYR A:256 , TYR A:257 , MET A:258 , ARG A:259 , PHE A:262 , PHE A:264 , GLY A:265 , CYS A:268 , LEU A:269 , PHE A:323 , LYS A:324 , HOH A:2022 , HOH A:2025 , HOH A:2039 , HOH A:2095 , HOH A:2115 , HOH A:2242 , HOH A:2243 , 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
BINDING SITE FOR RESIDUE GDX A 2006
09
AC9
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 , TYR D:256 , TYR D:257 , MET 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:2027 , HOH D:2042 , HOH D:2050 , HOH D:2051 , HOH D:2066 , HOH D:2183 , HOH D:2255
BINDING SITE FOR RESIDUE GDX D 2007
10
BC1
SOFTWARE
LEU C:251 , TYR C:256 , TYR C:257 , MET C:258 , ARG C:259 , PHE C:262 , PHE C:264 , GLY C:265 , CYS C:268 , PHE C:323 , LYS C:324 , ACY C:2009 , ACY C:2010 , HOH C:2080 , 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:2073 , HOH D:2083 , HOH D:2086 , HOH D:2144 , HOH D:2341 , HOH D:2345 , HOH D:2396
BINDING SITE FOR RESIDUE GDX D 2008
11
BC2
SOFTWARE
ARG C:259 , ACY C:2010 , GDX D:2008
BINDING SITE FOR RESIDUE ACY C 2009
12
BC3
SOFTWARE
ARG C:259 , PRO C:260 , VAL C:420 , ACY C:2009 , GDX D:2008
BINDING SITE FOR RESIDUE ACY C 2010
13
BC4
SOFTWARE
HOH C:2039 , LYS D:366
BINDING SITE FOR RESIDUE MPD C 2011
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(0, 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
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_d1mv8a1 (A:203-300)
1b: SCOP_d1mv8b1 (B:203-300)
1c: SCOP_d1mv8c1 (C:203-300)
1d: SCOP_d1mv8d1 (D:203-300)
2a: SCOP_d1mv8a3 (A:301-436)
2b: SCOP_d1mv8b3 (B:301-436)
2c: SCOP_d1mv8c3 (C:301-436)
2d: SCOP_d1mv8d3 (D:301-436)
3a: SCOP_d1mv8a2 (A:1-202)
3b: SCOP_d1mv8b2 (B:1-202)
3c: SCOP_d1mv8c2 (C:1-202)
3d: SCOP_d1mv8d2 (D:1-202)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
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
d1mv8a1
A:203-300
1b
d1mv8b1
B:203-300
1c
d1mv8c1
C:203-300
1d
d1mv8d1
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
d1mv8a3
A:301-436
2b
d1mv8b3
B:301-436
2c
d1mv8c3
C:301-436
2d
d1mv8d3
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
d1mv8a2
A:1-202
3b
d1mv8b2
B:1-202
3c
d1mv8c2
C:1-202
3d
d1mv8d2
D:1-202
[
close SCOP info
]
CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_1mv8A01 (A:1-202)
1b: CATH_1mv8B01 (B:1-202)
1c: CATH_1mv8A03 (A:235-436)
1d: CATH_1mv8B03 (B:235-436)
1e: CATH_1mv8C03 (C:235-436)
1f: CATH_1mv8D03 (D:235-436)
1g: CATH_1mv8C01 (C:1-202)
1h: CATH_1mv8D01 (D:1-202)
View:
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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
1mv8A01
A:1-202
1b
1mv8B01
B:1-202
1c
1mv8A03
A:235-436
1d
1mv8B03
B:235-436
1e
1mv8C03
C:235-436
1f
1mv8D03
D:235-436
1g
1mv8C01
C:1-202
1h
1mv8D01
D:1-202
[
close CATH info
]
Pfam Domains
(3, 12)
Info
all PFAM domains
1a: PFAM_UDPG_MGDP_dh_1mv8D01 (D:203-300)
1b: PFAM_UDPG_MGDP_dh_1mv8D02 (D:203-300)
1c: PFAM_UDPG_MGDP_dh_1mv8D03 (D:203-300)
1d: PFAM_UDPG_MGDP_dh_1mv8D04 (D:203-300)
2a: PFAM_UDPG_MGDP_dh_N_1mv8D05 (D:1-190)
2b: PFAM_UDPG_MGDP_dh_N_1mv8D06 (D:1-190)
2c: PFAM_UDPG_MGDP_dh_N_1mv8D07 (D:1-190)
2d: PFAM_UDPG_MGDP_dh_N_1mv8D08 (D:1-190)
3a: PFAM_UDPG_MGDP_dh_C_1mv8D09 (D:317-423)
3b: PFAM_UDPG_MGDP_dh_C_1mv8D10 (D:317-423)
3c: PFAM_UDPG_MGDP_dh_C_1mv8D11 (D:317-423)
3d: PFAM_UDPG_MGDP_dh_C_1mv8D12 (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-1mv8D01
D:203-300
1b
UDPG_MGDP_dh-1mv8D02
D:203-300
1c
UDPG_MGDP_dh-1mv8D03
D:203-300
1d
UDPG_MGDP_dh-1mv8D04
D:203-300
Clan
:
NADP_Rossmann
(1239)
Family
:
UDPG_MGDP_dh_N
(10)
Pseudomonas aeruginosa
(3)
2a
UDPG_MGDP_dh_N-1mv8D05
D:1-190
2b
UDPG_MGDP_dh_N-1mv8D06
D:1-190
2c
UDPG_MGDP_dh_N-1mv8D07
D:1-190
2d
UDPG_MGDP_dh_N-1mv8D08
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-1mv8D09
D:317-423
3b
UDPG_MGDP_dh_C-1mv8D10
D:317-423
3c
UDPG_MGDP_dh_C-1mv8D11
D:317-423
3d
UDPG_MGDP_dh_C-1mv8D12
D:317-423
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