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1MV8
Biol. Unit 2
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, 8)
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
2
Ligand/Ion
GUANOSINE 5'-(TRIHYDROGEN DIPHOSPHATE), P'-D-MANNOPYRANOSYL ESTER
3
MPD
1
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
4
NAD
2
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
5
SUC
1
Ligand/Ion
SUCROSE
[
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Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC5 (SOFTWARE)
4: AC6 (SOFTWARE)
5: AC9 (SOFTWARE)
6: BC1 (SOFTWARE)
7: BC2 (SOFTWARE)
8: BC3 (SOFTWARE)
9: BC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
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
2
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
3
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
4
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
5
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
6
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
7
BC2
SOFTWARE
ARG C:259 , ACY C:2010 , GDX D:2008
BINDING SITE FOR RESIDUE ACY C 2009
8
BC3
SOFTWARE
ARG C:259 , PRO C:260 , VAL C:420 , ACY C:2009 , GDX D:2008
BINDING SITE FOR RESIDUE ACY C 2010
9
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 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
;
View:
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Label:
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.
(no "Exon" information available for biological units yet)
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
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)
(
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(
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(
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Families
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(
)
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
[
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]
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)
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Topologies
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)
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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
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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