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3PDU
Asym. Unit
Info
Asym.Unit (736 KB)
Biol.Unit 1 (364 KB)
Biol.Unit 2 (363 KB)
Biol.Unit 3 (186 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF GAMMA-HYDROXYBUTYRATE DEHYDROGENASE FROM GEOBACTER SULFURREDUCENS IN COMPLEX WITH NADP+
Authors
:
Y. Zhang, R. M. Garavito
Date
:
25 Oct 10 (Deposition) - 11 Jan 12 (Release) - 01 Jun 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.89
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,G (2x)
Biol. Unit 3: F,H (1x)
Keywords
:
Gamma-Hydroxybutyrate Dehydrogenase, Succinic Semialdehyde Reductase, Glyoxylate Metabolism, Geobacter Sulfurreducens, Dehydrogenase/Reductase, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Zhang, Y. Zheng, L. Qin, S. Wang, G. W. Buchko, R. M. Garavito
Structural Characterization Of A Beta-Hydroxyacid Dehydrogenase From Geobacter Sulfurreducens And Geobacter Metallireducens With Succinic Semialdehyde Reductase Activity.
Biochimie V. 104 61 2014
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Hetero Components
(2, 19)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
1e: GLYCEROL (GOLe)
1f: GLYCEROL (GOLf)
1g: GLYCEROL (GOLg)
1h: GLYCEROL (GOLh)
1i: GLYCEROL (GOLi)
1j: GLYCEROL (GOLj)
1k: GLYCEROL (GOLk)
2a: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPa)
2b: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPb)
2c: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPc)
2d: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPd)
2e: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPe)
2f: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPf)
2g: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPg)
2h: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
11
Ligand/Ion
GLYCEROL
2
NAP
8
Ligand/Ion
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
[
close Hetero Component info
]
Sites
(19, 19)
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)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:8 , LEU A:9 , GLY A:10 , ILE A:11 , MET A:12 , ASN A:31 , ARG A:32 , ASN A:33 , MET A:64 , LEU A:65 , ALA A:66 , ALA A:70 , GLU A:73 , VAL A:74 , THR A:96 , VAL A:121 , GLY A:123 , THR A:124 , LYS A:125 , LYS A:171 , SER A:231 , PHE A:232 , PRO A:233 , HIS A:236 , LYS A:239 , HOH A:308 , HOH A:310 , HOH A:325 , HOH A:362 , HOH A:437 , HOH A:560 , HOH A:630 , HOH A:740 , HOH A:1011 , HOH A:1186 , HOH A:1423
BINDING SITE FOR RESIDUE NAP A 301
02
AC2
SOFTWARE
ARG A:250 , HOH A:410 , ARG B:242 , GLU B:246
BINDING SITE FOR RESIDUE GOL A 304
03
AC3
SOFTWARE
ARG A:242 , GLU A:246 , HOH A:754 , ARG B:250 , HOH B:1791 , HOH B:1797
BINDING SITE FOR RESIDUE GOL B 304
04
AC4
SOFTWARE
GLY B:8 , LEU B:9 , GLY B:10 , ILE B:11 , MET B:12 , ASN B:31 , ARG B:32 , ASN B:33 , MET B:64 , LEU B:65 , ALA B:66 , ALA B:70 , GLU B:73 , VAL B:74 , THR B:96 , VAL B:121 , GLY B:123 , THR B:124 , SER B:231 , PHE B:232 , HIS B:236 , LYS B:239 , HOH B:292 , HOH B:296 , HOH B:317 , HOH B:555 , HOH B:564 , HOH B:603 , HOH B:918 , HOH B:925 , HOH B:1116 , HOH B:1534 , HOH B:1589
BINDING SITE FOR RESIDUE NAP B 301
05
AC5
SOFTWARE
GLY B:131 , GLY B:155 , LYS B:156 , HOH B:303 , HOH B:312 , HOH B:539 , HOH B:541 , HOH B:760
BINDING SITE FOR RESIDUE GOL B 305
06
AC6
SOFTWARE
GLY C:8 , LEU C:9 , GLY C:10 , ILE C:11 , MET C:12 , ASN C:31 , ARG C:32 , ASN C:33 , MET C:64 , LEU C:65 , ALA C:66 , ALA C:70 , GLU C:73 , VAL C:74 , THR C:96 , VAL C:121 , GLY C:123 , THR C:124 , LYS C:171 , SER C:231 , PHE C:232 , HIS C:236 , LYS C:239 , HOH C:297 , HOH C:314 , HOH C:818 , HOH C:971 , HOH C:1099 , HOH C:1102 , HOH C:1510 , HOH C:1557 , HOH C:1567
BINDING SITE FOR RESIDUE NAP C 301
07
AC7
SOFTWARE
ARG C:242 , GLU C:246 , HOH C:474 , ARG D:250
BINDING SITE FOR RESIDUE GOL C 304
08
AC8
SOFTWARE
ARG C:250 , HOH C:581 , ARG D:242 , GLU D:246
BINDING SITE FOR RESIDUE GOL C 288
09
AC9
SOFTWARE
GLY D:8 , LEU D:9 , GLY D:10 , ILE D:11 , MET D:12 , ASN D:31 , ARG D:32 , ASN D:33 , LYS D:36 , MET D:64 , LEU D:65 , ALA D:66 , ALA D:70 , GLU D:73 , VAL D:74 , THR D:96 , VAL D:121 , GLY D:123 , THR D:124 , LYS D:171 , SER D:231 , PHE D:232 , PRO D:233 , HIS D:236 , LYS D:239 , HOH D:296 , HOH D:312 , HOH D:316 , HOH D:339 , HOH D:554 , HOH D:800 , HOH D:938 , HOH D:1097 , HOH D:1439
BINDING SITE FOR RESIDUE NAP D 301
10
BC1
SOFTWARE
GLU D:227 , PHE D:228 , PRO D:229 , GLU D:276 , HOH D:656 , ALA F:52 , ASN F:79
BINDING SITE FOR RESIDUE GOL D 305
11
BC2
SOFTWARE
GLY E:8 , LEU E:9 , GLY E:10 , ILE E:11 , MET E:12 , ASN E:31 , ARG E:32 , ASN E:33 , MET E:64 , LEU E:65 , ALA E:66 , ALA E:70 , GLU E:73 , VAL E:74 , THR E:96 , VAL E:121 , GLY E:123 , THR E:124 , SER E:231 , PHE E:232 , PRO E:233 , HIS E:236 , LYS E:239 , HOH E:317 , HOH E:451 , HOH E:913 , HOH E:1016 , HOH E:1081 , HOH E:1109 , HOH E:1132 , HOH E:1284 , HOH E:1498 , HOH E:1598
BINDING SITE FOR RESIDUE NAP E 301
12
BC3
SOFTWARE
ARG E:242 , GLU E:246 , HOH E:1345 , GLU G:246 , ARG G:250 , HOH G:717
BINDING SITE FOR RESIDUE GOL E 304
13
BC4
SOFTWARE
GLY F:8 , LEU F:9 , GLY F:10 , ILE F:11 , MET F:12 , ASN F:31 , ARG F:32 , ASN F:33 , MET F:64 , LEU F:65 , ALA F:66 , ALA F:70 , GLU F:73 , VAL F:74 , THR F:96 , VAL F:121 , GLY F:123 , THR F:124 , SER F:231 , PHE F:232 , PRO F:233 , HIS F:236 , LYS F:239 , HOH F:292 , HOH F:293 , HOH F:339 , HOH F:348 , HOH F:350 , HOH F:456 , HOH F:466 , HOH F:478 , HOH F:617 , HOH F:779 , HOH F:1009 , HOH F:1021
BINDING SITE FOR RESIDUE NAP F 301
14
BC5
SOFTWARE
ARG F:242 , GLU F:246 , HOH F:766 , ARG H:250
BINDING SITE FOR RESIDUE GOL F 304
15
BC6
SOFTWARE
GLU F:246 , ARG F:250 , HOH F:1104 , ARG H:242 , GLU H:246 , HOH H:330
BINDING SITE FOR RESIDUE GOL F 288
16
BC7
SOFTWARE
GLY G:8 , LEU G:9 , GLY G:10 , ILE G:11 , MET G:12 , ASN G:31 , ARG G:32 , ASN G:33 , MET G:64 , LEU G:65 , ALA G:66 , ALA G:70 , GLU G:73 , VAL G:74 , THR G:96 , VAL G:121 , GLY G:123 , THR G:124 , LYS G:171 , SER G:231 , PHE G:232 , PRO G:233 , HIS G:236 , LYS G:239 , HOH G:294 , HOH G:593 , HOH G:857 , HOH G:1495
BINDING SITE FOR RESIDUE NAP G 301
17
BC8
SOFTWARE
ARG E:250 , HOH E:1178 , ARG G:242 , GLU G:246
BINDING SITE FOR RESIDUE GOL G 304
18
BC9
SOFTWARE
HOH B:541 , HOH B:773 , ASN H:19 , ASP H:130 , ALA H:152 , ALA H:153 , HOH H:477 , HOH H:540 , HOH H:1018
BINDING SITE FOR RESIDUE GOL H 305
19
CC1
SOFTWARE
GLY H:8 , LEU H:9 , GLY H:10 , ILE H:11 , MET H:12 , ASN H:31 , ARG H:32 , ASN H:33 , MET H:64 , LEU H:65 , ALA H:66 , ALA H:70 , GLU H:73 , VAL H:74 , THR H:96 , VAL H:121 , GLY H:123 , THR H:124 , SER H:231 , PHE H:232 , PRO H:233 , HIS H:236 , LYS H:239 , HOH H:314 , HOH H:319 , HOH H:321 , HOH H:322 , HOH H:325 , HOH H:331 , HOH H:395 , HOH H:484 , HOH H:759 , HOH H:876 , HOH H:1064 , HOH H:1206
BINDING SITE FOR RESIDUE NAP H 301
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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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
(2, 16)
Info
All SCOP Domains
1a: SCOP_d3pdua2 (A:164-287)
1b: SCOP_d3pdub2 (B:164-287)
1c: SCOP_d3pduc2 (C:164-287)
1d: SCOP_d3pdud2 (D:164-287)
1e: SCOP_d3pdue2 (E:164-287)
1f: SCOP_d3pduf2 (F:164-287)
1g: SCOP_d3pdug2 (G:164-286)
1h: SCOP_d3pduh2 (H:164-287)
2a: SCOP_d3pdua1 (A:1-163)
2b: SCOP_d3pdub1 (B:2-163)
2c: SCOP_d3pduc1 (C:2-163)
2d: SCOP_d3pdud1 (D:1-163)
2e: SCOP_d3pdue1 (E:1-163)
2f: SCOP_d3pduf1 (F:2-163)
2g: SCOP_d3pdug1 (G:3-163)
2h: SCOP_d3pduh1 (H:2-163)
View:
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Classes
(
)
(
)
Folds
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(
)
Superfamilies
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(
)
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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
:
automated matches
(50)
Protein domain
:
automated matches
(50)
Geobacter sulfurreducens [TaxId: 35554]
(1)
1a
d3pdua2
A:164-287
1b
d3pdub2
B:164-287
1c
d3pduc2
C:164-287
1d
d3pdud2
D:164-287
1e
d3pdue2
E:164-287
1f
d3pduf2
F:164-287
1g
d3pdug2
G:164-286
1h
d3pduh2
H:164-287
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
:
automated matches
(447)
Protein domain
:
automated matches
(447)
Geobacter sulfurreducens [TaxId: 35554]
(1)
2a
d3pdua1
A:1-163
2b
d3pdub1
B:2-163
2c
d3pduc1
C:2-163
2d
d3pdud1
D:1-163
2e
d3pdue1
E:1-163
2f
d3pduf1
F:2-163
2g
d3pdug1
G:3-163
2h
d3pduh1
H:2-163
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(0, 0)
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Sorry, no Info available
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