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3KB6
Asym. Unit
Info
Asym.Unit (256 KB)
Biol.Unit 1 (246 KB)
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Title
:
CRYSTAL STRUCTURE OF D-LACTATE DEHYDROGENASE FROM AQUIFEX AEOLICUS COMPLEXED WITH NAD AND LACTIC ACID
Authors
:
S. V. Antonyuk, R. W. Strange, M. J. Ellis, Y. Bessho, S. Kuramitsu, S. Yo S. S. Hasnain, Riken Structural Genomics/Proteomics Initiative
Date
:
20 Oct 09 (Deposition) - 10 Nov 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.12
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Oxidoreductase, D-Ldh, Nad, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. V. Antonyuk, R. W. Strange, M. J. Ellis, Y. Bessho, S. Kuramitsu, Y. Inoue, S. Yokoyama, S. S. Hasnain
Structure Of D-Lactate Dehydrogenase From Aquifex Aeolicus Complexed With Nad(+) And Lactic Acid (Or Pyruvate).
Acta Crystallogr. , Sect. F V. 65 1209 2009
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Hetero Components
(7, 69)
Info
All Hetero Components
1a: PENTAETHYLENE GLYCOL (1PEa)
1b: PENTAETHYLENE GLYCOL (1PEb)
1c: PENTAETHYLENE GLYCOL (1PEc)
1d: PENTAETHYLENE GLYCOL (1PEd)
1e: PENTAETHYLENE GLYCOL (1PEe)
1f: PENTAETHYLENE GLYCOL (1PEf)
1g: PENTAETHYLENE GLYCOL (1PEg)
1h: PENTAETHYLENE GLYCOL (1PEh)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
2h: GLYCEROL (GOLh)
2i: GLYCEROL (GOLi)
2j: GLYCEROL (GOLj)
2k: GLYCEROL (GOLk)
3a: LACTIC ACID (LACa)
3b: LACTIC ACID (LACb)
3c: LACTIC ACID (LACc)
3d: LACTIC ACID (LACd)
4a: SELENOMETHIONINE (MSEa)
4aa: SELENOMETHIONINE (MSEaa)
4b: SELENOMETHIONINE (MSEb)
4c: SELENOMETHIONINE (MSEc)
4d: SELENOMETHIONINE (MSEd)
4e: SELENOMETHIONINE (MSEe)
4f: SELENOMETHIONINE (MSEf)
4g: SELENOMETHIONINE (MSEg)
4h: SELENOMETHIONINE (MSEh)
4i: SELENOMETHIONINE (MSEi)
4j: SELENOMETHIONINE (MSEj)
4k: SELENOMETHIONINE (MSEk)
4l: SELENOMETHIONINE (MSEl)
4m: SELENOMETHIONINE (MSEm)
4n: SELENOMETHIONINE (MSEn)
4o: SELENOMETHIONINE (MSEo)
4p: SELENOMETHIONINE (MSEp)
4q: SELENOMETHIONINE (MSEq)
4r: SELENOMETHIONINE (MSEr)
4s: SELENOMETHIONINE (MSEs)
4t: SELENOMETHIONINE (MSEt)
4u: SELENOMETHIONINE (MSEu)
4v: SELENOMETHIONINE (MSEv)
4w: SELENOMETHIONINE (MSEw)
4x: SELENOMETHIONINE (MSEx)
4y: SELENOMETHIONINE (MSEy)
4z: SELENOMETHIONINE (MSEz)
5a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
5b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
5c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
5d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
6a: DI(HYDROXYETHYL)ETHER (PEGa)
6b: DI(HYDROXYETHYL)ETHER (PEGb)
6c: DI(HYDROXYETHYL)ETHER (PEGc)
6d: DI(HYDROXYETHYL)ETHER (PEGd)
6e: DI(HYDROXYETHYL)ETHER (PEGe)
6f: DI(HYDROXYETHYL)ETHER (PEGf)
6g: DI(HYDROXYETHYL)ETHER (PEGg)
6h: DI(HYDROXYETHYL)ETHER (PEGh)
6i: DI(HYDROXYETHYL)ETHER (PEGi)
6j: DI(HYDROXYETHYL)ETHER (PEGj)
7a: PROPANOIC ACID (PPIa)
7b: PROPANOIC ACID (PPIb)
7c: PROPANOIC ACID (PPIc)
7d: PROPANOIC ACID (PPId)
7e: PROPANOIC ACID (PPIe)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
1PE
8
Ligand/Ion
PENTAETHYLENE GLYCOL
2
GOL
11
Ligand/Ion
GLYCEROL
3
LAC
4
Ligand/Ion
LACTIC ACID
4
MSE
27
Mod. Amino Acid
SELENOMETHIONINE
5
NAD
4
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
6
PEG
10
Ligand/Ion
DI(HYDROXYETHYL)ETHER
7
PPI
5
Ligand/Ion
PROPANOIC ACID
[
close Hetero Component info
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Sites
(42, 42)
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)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
42: EC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PRO A:9 , ARG A:71 , TYR A:297 , HOH A:450
BINDING SITE FOR RESIDUE PPI A 398
02
AC2
SOFTWARE
PHE A:49 , SER A:72 , VAL A:73 , GLY A:74 , TYR A:96 , ARG A:231 , HIS A:294 , NAD A:400
BINDING SITE FOR RESIDUE LAC A 399
03
AC3
SOFTWARE
VAL A:73 , TYR A:96 , VAL A:101 , GLY A:150 , ARG A:151 , ILE A:152 , TYR A:170 , ASP A:171 , VAL A:172 , HIS A:201 , PRO A:203 , THR A:208 , THR A:229 , ALA A:230 , ARG A:231 , ASP A:255 , HIS A:294 , ALA A:296 , TYR A:297 , LAC A:399 , HOH A:405 , HOH A:406 , HOH A:407 , HOH A:416 , HOH A:417 , HOH A:437 , HOH A:449 , HOH A:471 , PEG A:701 , GOL A:710 , HOH C:408 , HOH C:462 , PEG C:702
BINDING SITE FOR RESIDUE NAD A 400
04
AC4
SOFTWARE
ARG A:137 , ASP A:196 , ASP A:222 , GLY A:223
BINDING SITE FOR RESIDUE PEG A 403
05
AC5
SOFTWARE
ASP A:171 , VAL A:172 , LYS A:174 , THR A:186 , HOH A:426 , GLU C:190
BINDING SITE FOR RESIDUE 1PE A 404
06
AC6
SOFTWARE
VAL A:50 , TYR A:51 , ASP A:76 , ARG A:231 , GLU A:260 , HIS A:294 , HOH A:533
BINDING SITE FOR RESIDUE PPI A 453
07
AC7
SOFTWARE
PRO A:63 , LYS A:66 , LYS A:86 , GLY A:87 , HOH A:597
BINDING SITE FOR RESIDUE PEG A 454
08
AC8
SOFTWARE
THR A:143 , LYS A:166 , GLU A:194 , ASP A:196 , LYS A:221 , HOH A:595
BINDING SITE FOR RESIDUE 1PE A 444
09
AC9
SOFTWARE
PHE A:75 , ASP A:76 , ILE A:78 , ASP A:79 , LEU A:80 , ASP A:81 , HOH A:423 , HOH A:470 , HOH C:495
BINDING SITE FOR RESIDUE PEG A 555
10
BC1
SOFTWARE
GLU A:37 , LEU A:58 , LYS A:61 , HOH A:618
BINDING SITE FOR RESIDUE 1PE A 700
11
BC2
SOFTWARE
GLU A:207 , ARG A:216 , NAD A:400 , PEG A:802
BINDING SITE FOR RESIDUE GOL A 710
12
BC3
SOFTWARE
LYS A:53 , LEU A:54 , THR A:55 , ASP A:76 , HIS A:77
BINDING SITE FOR RESIDUE GOL A 800
13
BC4
SOFTWARE
GLU A:99 , LEU B:161 , ALA B:162 , 1PE B:804
BINDING SITE FOR RESIDUE 1PE A 335
14
BC5
SOFTWARE
THR A:149 , GLY A:150 , ASP A:171 , VAL A:173 , ARG A:175 , NAD A:400 , LYS C:174 , LYS C:179 , 1PE C:404 , HOH C:408 , PEG C:702
BINDING SITE FOR RESIDUE PEG A 701
15
BC6
SOFTWARE
HIS A:210 , ASN A:213 , ARG A:216 , HOH A:481 , GOL A:710
BINDING SITE FOR RESIDUE PEG A 802
16
BC7
SOFTWARE
GLY A:164 , 1PE B:804
BINDING SITE FOR RESIDUE PEG A 803
17
BC8
SOFTWARE
VAL A:123 , LYS A:124 , LEU A:126 , LEU B:281 , CYS B:285 , LEU C:281 , CYS C:285 , LYS D:124 , LEU D:126
BINDING SITE FOR RESIDUE PEG A 772
18
BC9
SOFTWARE
TYR A:51 , ILE A:264 , SER B:129 , GLN B:130
BINDING SITE FOR RESIDUE GOL B 711
19
CC1
SOFTWARE
ARG B:71 , TYR B:297 , ILE B:306 , HOH B:483 , HOH B:522
BINDING SITE FOR RESIDUE PPI B 398
20
CC2
SOFTWARE
PHE B:49 , SER B:72 , VAL B:73 , GLY B:74 , TYR B:96 , ARG B:231 , HIS B:294 , NAD B:400
BINDING SITE FOR RESIDUE LAC B 399
21
CC3
SOFTWARE
VAL B:73 , TYR B:96 , VAL B:101 , GLY B:150 , ARG B:151 , ILE B:152 , TYR B:170 , ASP B:171 , VAL B:172 , HIS B:201 , PRO B:203 , THR B:208 , THR B:229 , ALA B:230 , ARG B:231 , ASP B:255 , HIS B:294 , ALA B:296 , TYR B:297 , LAC B:399 , HOH B:401 , HOH B:402 , HOH B:405 , HOH B:408 , HOH B:423 , HOH B:425 , HOH B:448 , HOH B:457 , HOH B:553 , HOH B:603 , HOH B:657
BINDING SITE FOR RESIDUE NAD B 400
22
CC4
SOFTWARE
LYS B:53 , HIS B:77 , ILE B:78 , ASP B:79
BINDING SITE FOR RESIDUE GOL B 770
23
CC5
SOFTWARE
SER B:33 , GLU B:37 , GLU B:57 , LEU B:58 , LYS B:61
BINDING SITE FOR RESIDUE 1PE B 407
24
CC6
SOFTWARE
TYR B:170 , VAL B:172 , LYS B:174 , LYS B:179 , TYR B:185
BINDING SITE FOR RESIDUE 1PE B 404
25
CC7
SOFTWARE
PHE B:15 , ASP B:222 , GLY B:223 , GLY B:247 , HOH B:585
BINDING SITE FOR RESIDUE GOL B 777
26
CC8
SOFTWARE
LYS A:124 , LYS B:117 , ASP B:121 , ALA B:284 , CYS B:285 , LYS D:125
BINDING SITE FOR RESIDUE GOL B 800
27
CC9
SOFTWARE
GLY A:247 , GLU B:207 , HIS B:209 , MSE B:211 , ASN B:213 , ARG B:216
BINDING SITE FOR RESIDUE GOL B 801
28
DC1
SOFTWARE
ALA A:162 , 1PE A:335 , PEG A:803 , MSE B:158 , TYR B:159 , LEU B:161 , ALA B:162
BINDING SITE FOR RESIDUE 1PE B 804
29
DC2
SOFTWARE
VAL A:172 , VAL A:173 , NAD A:400 , PEG A:701 , LYS C:179 , VAL C:184 , TYR C:185 , HOH C:483
BINDING SITE FOR RESIDUE PEG C 702
30
DC3
SOFTWARE
SER C:7 , ARG C:71 , TYR C:297 , HOH C:468 , HOH D:582
BINDING SITE FOR RESIDUE PPI C 398
31
DC4
SOFTWARE
PHE C:49 , SER C:72 , VAL C:73 , GLY C:74 , TYR C:96 , ARG C:231 , HIS C:294 , NAD C:400
BINDING SITE FOR RESIDUE LAC C 399
32
DC5
SOFTWARE
VAL C:73 , TYR C:96 , VAL C:101 , THR C:149 , GLY C:150 , ARG C:151 , ILE C:152 , TYR C:170 , ASP C:171 , VAL C:172 , HIS C:201 , PRO C:203 , THR C:208 , THR C:229 , ALA C:230 , ARG C:231 , ASP C:255 , HIS C:294 , ALA C:296 , TYR C:297 , LAC C:399 , HOH C:407 , HOH C:410 , HOH C:417 , HOH C:426 , HOH C:451 , HOH C:467 , HOH C:480 , HOH C:487 , HOH C:511 , HOH C:516 , HOH C:533
BINDING SITE FOR RESIDUE NAD C 400
33
DC6
SOFTWARE
GLU C:99 , GLY D:164
BINDING SITE FOR RESIDUE GOL C 401
34
DC7
SOFTWARE
VAL A:173 , LYS A:174 , ARG A:175 , GLU A:176 , HOH A:498 , PEG A:701 , TYR C:170 , ASP C:171 , VAL C:172 , LYS C:174 , THR C:186 , SER C:187
BINDING SITE FOR RESIDUE 1PE C 404
35
DC8
SOFTWARE
THR C:55 , ASP C:76 , HIS C:77 , ASP C:79
BINDING SITE FOR RESIDUE GOL C 650
36
DC9
SOFTWARE
TYR C:170 , ARG C:216
BINDING SITE FOR RESIDUE PEG C 771
37
EC1
SOFTWARE
ARG D:71 , TYR D:297 , HOH D:579
BINDING SITE FOR RESIDUE PPI D 398
38
EC2
SOFTWARE
PHE D:49 , VAL D:50 , SER D:72 , VAL D:73 , GLY D:74 , TYR D:96 , ARG D:231 , HIS D:294 , NAD D:400
BINDING SITE FOR RESIDUE LAC D 399
39
EC3
SOFTWARE
VAL D:73 , TYR D:96 , VAL D:101 , GLY D:150 , ARG D:151 , ILE D:152 , TYR D:170 , ASP D:171 , VAL D:172 , HIS D:201 , VAL D:202 , PRO D:203 , THR D:208 , THR D:229 , ALA D:230 , ARG D:231 , ASP D:255 , HIS D:294 , ALA D:296 , TYR D:297 , LAC D:399 , HOH D:410 , HOH D:413 , HOH D:420 , HOH D:428 , HOH D:435 , HOH D:438 , HOH D:443 , HOH D:477 , HOH D:486 , HOH D:496 , HOH D:507 , HOH D:529 , HOH D:570
BINDING SITE FOR RESIDUE NAD D 400
40
EC4
SOFTWARE
ASP D:222 , ARG D:246
BINDING SITE FOR RESIDUE GOL D 401
41
EC5
SOFTWARE
LEU D:54 , ASP D:76 , HIS D:77 , ASP D:79
BINDING SITE FOR RESIDUE GOL D 777
42
EC6
SOFTWARE
PRO D:63 , LEU D:65 , LYS D:86
BINDING SITE FOR RESIDUE PEG D 405
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
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Exons
(0, 0)
Info
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(0, 0)
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CATH Domains
(0, 0)
Info
all CATH domains
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Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_2_Hacid_dh_3kb6D01 (D:3-328)
1b: PFAM_2_Hacid_dh_3kb6D02 (D:3-328)
1c: PFAM_2_Hacid_dh_3kb6D03 (D:3-328)
1d: PFAM_2_Hacid_dh_3kb6D04 (D:3-328)
2a: PFAM_2_Hacid_dh_C_3kb6D05 (D:106-296)
2b: PFAM_2_Hacid_dh_C_3kb6D06 (D:106-296)
2c: PFAM_2_Hacid_dh_C_3kb6D07 (D:106-296)
2d: PFAM_2_Hacid_dh_C_3kb6D08 (D:106-296)
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Clans
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Clan
:
Form_Glyc_dh
(56)
Family
:
2-Hacid_dh
(21)
Aquifex aeolicus
(1)
1a
2-Hacid_dh-3kb6D01
D:3-328
1b
2-Hacid_dh-3kb6D02
D:3-328
1c
2-Hacid_dh-3kb6D03
D:3-328
1d
2-Hacid_dh-3kb6D04
D:3-328
Clan
:
NADP_Rossmann
(1239)
Family
:
2-Hacid_dh_C
(23)
Aquifex aeolicus
(1)
2a
2-Hacid_dh_C-3kb6D05
D:106-296
2b
2-Hacid_dh_C-3kb6D06
D:106-296
2c
2-Hacid_dh_C-3kb6D07
D:106-296
2d
2-Hacid_dh_C-3kb6D08
D:106-296
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