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5V7N
Asym. Unit
Info
Asym.Unit (439 KB)
Biol.Unit 1 (216 KB)
Biol.Unit 2 (215 KB)
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Title
:
CRYSTAL STRUCTURE OF NADPH-DEPENDENT GLYOXYLATE/HYDROXYPYRUVATE REDUCTASE SMC04462 (SMGHRB) FROM SINORHIZOBIUM MELILOTI IN COMPLEX WITH NADP AND 2-KETO-D-GLUCONIC ACID
Authors
:
I. G. Shabalin, K. B. Handing, C. D. Miks, J. Kutner, D. Matelska, J. Bona S. C. Almo, W. Minor, New York Structural Genomics Research Cons (Nysgrc)
Date
:
20 Mar 17 (Deposition) - 29 Mar 17 (Release) - 29 Mar 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.75
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase, Nadp, Nysgrc, Sinorhizobium Meliloti, Structural Genomics, Psi-Biology, New York Structural Genomics Research Consortium, Oxidoreductase
(Keyword Search:
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Reference
:
I. G. Shabalin, K. B. Handing, W. Minor
Evolutionary, Biochemical, And Structural Studies On D-2-Hydroxyacid Dehydrogenases From Sinorhizium Meliloti 1021 Indicate A Subdivision Of The Glyoxylate/Hydroxypyruvate Reductases
To Be Published
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Hetero Components
(8, 31)
Info
All Hetero Components
1a: 2-KETO-D-GLUCONIC ACID (8YVa)
1b: 2-KETO-D-GLUCONIC ACID (8YVb)
1c: 2-KETO-D-GLUCONIC ACID (8YVc)
1d: 2-KETO-D-GLUCONIC ACID (8YVd)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
2e: CHLORIDE ION (CLe)
2f: CHLORIDE ION (CLf)
2g: CHLORIDE ION (CLg)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
4c: MAGNESIUM ION (MGc)
4d: MAGNESIUM ION (MGd)
4e: MAGNESIUM ION (MGe)
4f: MAGNESIUM ION (MGf)
4g: MAGNESIUM ION (MGg)
6a: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPa)
6b: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPb)
6c: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPc)
6d: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPd)
5a: SODIUM ION (NAa)
5b: SODIUM ION (NAb)
5c: SODIUM ION (NAc)
5d: SODIUM ION (NAd)
7a: DI(HYDROXYETHYL)ETHER (PEGa)
7b: DI(HYDROXYETHYL)ETHER (PEGb)
8a: TETRAETHYLENE GLYCOL (PG4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
8YV
4
Ligand/Ion
2-KETO-D-GLUCONIC ACID
2
CL
7
Ligand/Ion
CHLORIDE ION
3
GOL
2
Ligand/Ion
GLYCEROL
4
MG
7
Ligand/Ion
MAGNESIUM ION
5
NA
4
Ligand/Ion
SODIUM ION
6
NAP
4
Ligand/Ion
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
7
PEG
2
Ligand/Ion
DI(HYDROXYETHYL)ETHER
8
PG4
1
Ligand/Ion
TETRAETHYLENE GLYCOL
[
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Sites
(31, 31)
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: AD1 (SOFTWARE)
11: AD2 (SOFTWARE)
12: AD3 (SOFTWARE)
13: AD4 (SOFTWARE)
14: AD5 (SOFTWARE)
15: AD6 (SOFTWARE)
16: AD7 (SOFTWARE)
17: AD8 (SOFTWARE)
18: AD9 (SOFTWARE)
19: AE1 (SOFTWARE)
20: AE2 (SOFTWARE)
21: AE3 (SOFTWARE)
22: AE4 (SOFTWARE)
23: AE5 (SOFTWARE)
24: AE6 (SOFTWARE)
25: AE7 (SOFTWARE)
26: AE8 (SOFTWARE)
27: AE9 (SOFTWARE)
28: AF1 (SOFTWARE)
29: AF2 (SOFTWARE)
30: AF3 (SOFTWARE)
31: AF4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
VAL A:72 , VAL A:100 , PHE A:148 , LEU A:150 , GLY A:151 , ARG A:152 , ILE A:153 , THR A:172 , ARG A:173 , THR A:174 , ILE A:200 , VAL A:201 , PRO A:202 , SER A:206 , THR A:207 , VAL A:228 , GLY A:229 , ARG A:230 , ASP A:254 , HIS A:277 , ALA A:279 , 8YV A:402 , MG A:408 , HOH A:508 , HOH A:545 , HOH A:555 , HOH A:576 , HOH A:583 , HOH A:608 , HOH A:610 , HOH A:621 , HOH A:624 , HOH A:634 , HOH A:642 , HOH A:655 , HOH A:659 , HOH A:696 , HOH A:724
binding site for residue NAP A 401
02
AC2
SOFTWARE
SER A:50 , GLY A:51 , PHE A:70 , GLY A:71 , VAL A:72 , GLY A:73 , LEU A:96 , ARG A:230 , HIS A:277 , SER A:280 , ARG A:286 , MET A:289 , NAP A:401 , HOH A:515 , HOH A:598 , HOH A:690
binding site for residue 8YV A 402
03
AC3
SOFTWARE
ALA A:191 , GLU A:192 , VAL A:194 , ALA A:218 , LEU A:219 , HOH A:626
binding site for residue NA A 403
04
AC4
SOFTWARE
ARG A:28 , GLU A:30 , PRO A:137 , PG4 A:407 , HOH A:732 , VAL B:283
binding site for residue PEG A 404
05
AC5
SOFTWARE
ASN A:13 , ARG A:286 , HOH A:779
binding site for residue CL A 405
06
AC6
SOFTWARE
ALA A:34
binding site for residue CL A 406
07
AC7
SOFTWARE
LYS A:11 , GLU A:30 , PRO A:134 , PRO A:137 , PEG A:404 , HOH A:582
binding site for residue PG4 A 407
08
AC8
SOFTWARE
NAP A:401 , HOH A:724 , HOH A:738 , HOH A:746 , HOH A:763 , HOH A:812
binding site for residue MG A 408
09
AC9
SOFTWARE
HOH A:527 , HOH A:595 , HOH A:800 , HOH A:802 , HOH A:830 , HOH A:860
binding site for residue MG A 409
10
AD1
SOFTWARE
VAL B:72 , VAL B:100 , PHE B:148 , LEU B:150 , GLY B:151 , ARG B:152 , ILE B:153 , THR B:172 , ARG B:173 , THR B:174 , ILE B:200 , VAL B:201 , PRO B:202 , SER B:206 , THR B:207 , VAL B:228 , GLY B:229 , ARG B:230 , ASP B:254 , HIS B:277 , ALA B:279 , 8YV B:402 , MG B:408 , HOH B:518 , HOH B:522 , HOH B:525 , HOH B:538 , HOH B:560 , HOH B:584 , HOH B:601 , HOH B:604 , HOH B:605 , HOH B:616 , HOH B:623 , HOH B:660 , HOH B:682 , HOH B:710 , HOH B:723
binding site for residue NAP B 401
11
AD2
SOFTWARE
SER B:50 , GLY B:51 , PHE B:70 , GLY B:71 , VAL B:72 , GLY B:73 , LEU B:96 , ARG B:230 , HIS B:277 , SER B:280 , ARG B:286 , MET B:289 , NAP B:401 , HOH B:528 , HOH B:598 , HOH B:658
binding site for residue 8YV B 402
12
AD3
SOFTWARE
ALA B:191 , GLU B:192 , VAL B:194 , ALA B:218 , LEU B:219 , HOH B:724
binding site for residue NA B 403
13
AD4
SOFTWARE
ASN B:13 , ARG B:286 , HOH B:763 , HOH B:773
binding site for residue CL B 404
14
AD5
SOFTWARE
ALA B:34
binding site for residue CL B 405
15
AD6
SOFTWARE
VAL B:95 , THR B:285 , ALA B:288 , HOH B:504 , HOH B:526 , HOH B:665
binding site for residue GOL B 406
16
AD7
SOFTWARE
HOH A:702 , HOH A:717 , HOH A:744 , ALA B:319 , HOH B:681 , HOH B:725
binding site for residue MG B 407
17
AD8
SOFTWARE
NAP B:401 , HOH B:616 , HOH B:710 , HOH B:723 , HOH B:739 , HOH B:808
binding site for residue MG B 408
18
AD9
SOFTWARE
VAL C:72 , VAL C:100 , PHE C:148 , GLY C:149 , LEU C:150 , GLY C:151 , ARG C:152 , ILE C:153 , THR C:172 , ARG C:173 , THR C:174 , ILE C:200 , VAL C:201 , PRO C:202 , SER C:206 , THR C:207 , VAL C:228 , GLY C:229 , ARG C:230 , ASP C:254 , HIS C:277 , ALA C:279 , 8YV C:402 , MG C:405 , HOH C:505 , HOH C:506 , HOH C:511 , HOH C:512 , HOH C:529 , HOH C:533 , HOH C:547 , HOH C:550 , HOH C:558 , HOH C:565 , HOH C:598 , HOH C:617 , HOH C:618 , HOH C:626 , HOH C:628 , HOH C:629 , HOH C:654
binding site for residue NAP C 401
19
AE1
SOFTWARE
GLY C:51 , PHE C:70 , GLY C:71 , VAL C:72 , GLY C:73 , LEU C:96 , ARG C:230 , HIS C:277 , SER C:280 , ARG C:286 , MET C:289 , NAP C:401 , HOH C:514 , HOH C:548 , HOH C:602 , HOH C:624
binding site for residue 8YV C 402
20
AE2
SOFTWARE
ALA C:191 , GLU C:192 , VAL C:194 , ALA C:218 , LEU C:219 , HOH C:643
binding site for residue NA C 403
21
AE3
SOFTWARE
ASN C:13 , ARG C:286
binding site for residue CL C 404
22
AE4
SOFTWARE
NAP C:401 , HOH C:533 , HOH C:618 , HOH C:628 , HOH C:716 , HOH C:770
binding site for residue MG C 405
23
AE5
SOFTWARE
VAL D:72 , VAL D:100 , PHE D:148 , LEU D:150 , GLY D:151 , ARG D:152 , ILE D:153 , THR D:172 , ARG D:173 , THR D:174 , ILE D:200 , VAL D:201 , PRO D:202 , SER D:206 , THR D:207 , VAL D:228 , GLY D:229 , ARG D:230 , ASP D:254 , HIS D:277 , ALA D:279 , 8YV D:402 , MG D:408 , HOH D:519 , HOH D:533 , HOH D:535 , HOH D:536 , HOH D:537 , HOH D:550 , HOH D:557 , HOH D:562 , HOH D:566 , HOH D:577 , HOH D:591 , HOH D:620 , HOH D:629 , HOH D:636 , HOH D:651 , HOH D:676 , HOH D:684
binding site for residue NAP D 401
24
AE6
SOFTWARE
SER D:50 , GLY D:51 , PHE D:70 , GLY D:71 , VAL D:72 , GLY D:73 , LEU D:96 , ARG D:230 , HIS D:277 , SER D:280 , ARG D:286 , MET D:289 , NAP D:401 , HOH D:565 , HOH D:609 , HOH D:657
binding site for residue 8YV D 402
25
AE7
SOFTWARE
ALA D:191 , GLU D:192 , VAL D:194 , ALA D:218 , LEU D:219 , HOH D:705
binding site for residue NA D 403
26
AE8
SOFTWARE
VAL C:283 , GLU D:30 , PRO D:137 , LYS D:222 , HOH D:679
binding site for residue PEG D 404
27
AE9
SOFTWARE
ASN D:13 , ARG D:286 , HOH D:707 , HOH D:724
binding site for residue CL D 405
28
AF1
SOFTWARE
ALA D:34
binding site for residue CL D 406
29
AF2
SOFTWARE
VAL D:95 , THR D:285 , ALA D:288 , HOH D:517
binding site for residue GOL D 407
30
AF3
SOFTWARE
NAP D:401 , HOH D:519 , HOH D:620 , HOH D:684 , HOH D:692 , HOH D:770
binding site for residue MG D 408
31
AF4
SOFTWARE
HOH D:597 , HOH D:633 , HOH D:761 , HOH D:771 , HOH D:804
binding site for residue MG D 409
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are not available)
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PROSITE Patterns/Profiles
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Exons
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SCOP Domains
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CATH Domains
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Pfam Domains
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