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3GDP
Asym. Unit
Info
Asym.Unit (210 KB)
Biol.Unit 1 (105 KB)
Biol.Unit 2 (104 KB)
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(1)
Title
:
HYDROXYNITRILE LYASE FROM ALMOND, MONOCLINIC CRYSTAL FORM
Authors
:
I. Dreveny, K. Gruber, C. Kratky
Date
:
24 Feb 09 (Deposition) - 24 Mar 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.57
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Hydroxynitrile Lyase, Flavin, Gmc Oxidoreductase, Almond, Cyanogenesis, Flavoprotein, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
I. Dreveny, A. S. Andryushkova, A. Glieder, K. Gruber, C. Kratky
Substrate Binding In The Fad-Dependent Hydroxynitrile Lyase From Almond Provides Insight Into The Mechanism Of Cyanohydrin Formation And Explains The Absence Of Dehydrogenation Activity.
Biochemistry V. 48 3370 2009
[
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Hetero Components
(8, 25)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
2a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
2b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
3a: ALPHA-L-FUCOSE (FUCa)
3b: ALPHA-L-FUCOSE (FUCb)
4a: BETA-L-FUCOSE (FULa)
5a: ISOPROPYL ALCOHOL (IPAa)
5b: ISOPROPYL ALCOHOL (IPAb)
6a: ALPHA-D-MANNOSE (MANa)
6b: ALPHA-D-MANNOSE (MANb)
6c: ALPHA-D-MANNOSE (MANc)
6d: ALPHA-D-MANNOSE (MANd)
7a: N-ACETYL-D-GLUCOSAMINE (NAGa)
7b: N-ACETYL-D-GLUCOSAMINE (NAGb)
7c: N-ACETYL-D-GLUCOSAMINE (NAGc)
7d: N-ACETYL-D-GLUCOSAMINE (NAGd)
7e: N-ACETYL-D-GLUCOSAMINE (NAGe)
7f: N-ACETYL-D-GLUCOSAMINE (NAGf)
7g: N-ACETYL-D-GLUCOSAMINE (NAGg)
7h: N-ACETYL-D-GLUCOSAMINE (NAGh)
7i: N-ACETYL-D-GLUCOSAMINE (NAGi)
7j: N-ACETYL-D-GLUCOSAMINE (NAGj)
7k: N-ACETYL-D-GLUCOSAMINE (NAGk)
8a: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
2
Ligand/Ion
BETA-D-MANNOSE
2
FAD
2
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
3
FUC
2
Ligand/Ion
ALPHA-L-FUCOSE
4
FUL
1
Ligand/Ion
BETA-L-FUCOSE
5
IPA
2
Ligand/Ion
ISOPROPYL ALCOHOL
6
MAN
4
Ligand/Ion
ALPHA-D-MANNOSE
7
NAG
11
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
8
NDG
1
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
[
close Hetero Component info
]
Sites
(25, 25)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ILE A:121 , SER A:125 , PHE A:490 , TYR A:492 , HOH A:866 , HOH A:1156 , HOH A:1176
BINDING SITE FOR RESIDUE IPA A 522
02
AC2
SOFTWARE
GLY A:33 , GLY A:35 , THR A:36 , SER A:37 , LEU A:54 , GLU A:55 , ARG A:56 , VAL A:98 , GLY A:100 , ARG A:101 , VAL A:102 , GLY A:105 , THR A:106 , ASN A:110 , ALA A:111 , GLY A:112 , VAL A:113 , ALA A:215 , VAL A:217 , SER A:256 , ALA A:257 , VAL A:379 , TRP A:458 , HIS A:459 , ASP A:486 , GLY A:487 , HIS A:497 , PRO A:498 , GLN A:499 , TYR A:502 , HOH A:593 , HOH A:694 , HOH A:777 , HOH A:831 , HOH A:835 , HOH A:845 , HOH A:853 , HOH A:879 , HOH A:920
BINDING SITE FOR RESIDUE FAD A 523
03
AC3
SOFTWARE
ASN A:118 , HIS A:177 , GLU A:179 , ASN A:323 , HOH A:632 , HOH A:827 , HOH A:925 , HOH A:1202 , HOH A:1299 , HOH A:1349
BINDING SITE FOR RESIDUE NAG A 524
04
AC4
SOFTWARE
ARG A:116 , ASP A:132 , ASN A:135 , ASP A:176 , NAG A:526 , FUL A:527 , HOH A:568 , HOH A:877 , HOH A:1088 , HOH A:1208 , HOH A:1213 , HOH A:1250
BINDING SITE FOR RESIDUE NAG A 525
05
AC5
SOFTWARE
THR A:119 , ASP A:176 , NAG A:525 , FUL A:527 , MAN A:528 , HOH A:538
BINDING SITE FOR RESIDUE NAG A 526
06
AC6
SOFTWARE
NAG A:525 , NAG A:526 , HOH A:568
BINDING SITE FOR RESIDUE FUL A 527
07
AC7
SOFTWARE
NAG A:526 , MAN A:529 , HOH A:554
BINDING SITE FOR RESIDUE MAN A 528
08
AC8
SOFTWARE
HIS A:171 , GLU A:178 , MAN A:528 , HOH A:588
BINDING SITE FOR RESIDUE MAN A 529
09
AC9
SOFTWARE
LEU A:366 , ASN A:392 , NAG A:531 , FUC A:532 , HOH A:587 , HOH A:683 , HOH A:784
BINDING SITE FOR RESIDUE NAG A 530
10
BC1
SOFTWARE
NAG A:530 , FUC A:532 , HOH A:686
BINDING SITE FOR RESIDUE NAG A 531
11
BC2
SOFTWARE
NAG A:530 , NAG A:531 , HOH A:683
BINDING SITE FOR RESIDUE FUC A 532
12
BC3
SOFTWARE
ASN A:352 , ASN A:430 , HOH A:570 , HOH A:650 , HOH A:824 , HOH A:1301
BINDING SITE FOR RESIDUE NAG A 533
13
BC4
SOFTWARE
ILE B:121 , PHE B:490 , TYR B:492 , HOH B:850 , HOH B:1002 , HOH B:1381
BINDING SITE FOR RESIDUE IPA B 522
14
BC5
SOFTWARE
GLY B:33 , GLY B:35 , THR B:36 , SER B:37 , LEU B:54 , GLU B:55 , ARG B:56 , VAL B:98 , GLY B:100 , ARG B:101 , VAL B:102 , GLY B:105 , THR B:106 , ASN B:110 , ALA B:111 , GLY B:112 , VAL B:113 , ALA B:215 , VAL B:217 , SER B:256 , ALA B:257 , VAL B:379 , TRP B:458 , HIS B:459 , ASP B:486 , GLY B:487 , HIS B:497 , PRO B:498 , GLN B:499 , TYR B:502 , HOH B:831 , HOH B:841 , HOH B:847 , HOH B:848 , HOH B:851 , HOH B:861 , HOH B:885 , HOH B:976 , HOH B:1058
BINDING SITE FOR RESIDUE FAD B 523
15
BC6
SOFTWARE
NAG B:525 , FUC B:526 , BMA B:527 , HOH B:1432
BINDING SITE FOR RESIDUE NAG B 524
16
BC7
SOFTWARE
LEU B:366 , ASN B:392 , NAG B:524 , FUC B:526 , HOH B:1007 , HOH B:1245
BINDING SITE FOR RESIDUE NAG B 525
17
BC8
SOFTWARE
NAG B:524 , NAG B:525 , HOH B:1277
BINDING SITE FOR RESIDUE FUC B 526
18
BC9
SOFTWARE
ASP A:422 , NAG B:524 , MAN B:528
BINDING SITE FOR RESIDUE BMA B 527
19
CC1
SOFTWARE
LYS A:416 , PRO A:417 , LYS A:419 , ASP A:422 , HOH A:607 , BMA B:527 , HOH B:535 , HOH B:590 , HOH B:625
BINDING SITE FOR RESIDUE MAN B 528
20
CC2
SOFTWARE
ARG B:116 , ASP B:132 , ASN B:135 , ASP B:176 , NAG B:530 , HOH B:866 , HOH B:880 , HOH B:1276 , HOH B:1283 , HOH B:1323
BINDING SITE FOR RESIDUE NAG B 529
21
CC3
SOFTWARE
GLU B:178 , NAG B:529 , BMA B:531 , HOH B:1341 , HOH B:1373
BINDING SITE FOR RESIDUE NAG B 530
22
CC4
SOFTWARE
NAG B:530 , MAN B:532 , HOH B:1291 , HOH B:1380
BINDING SITE FOR RESIDUE BMA B 531
23
CC5
SOFTWARE
HIS B:171 , GLU B:178 , BMA B:531 , HOH B:1097 , HOH B:1370
BINDING SITE FOR RESIDUE MAN B 532
24
CC6
SOFTWARE
ALA A:519 , HOH A:1267 , ASN B:352 , ASN B:430 , HOH B:1232 , HOH B:1502 , HOH B:1597
BINDING SITE FOR RESIDUE NDG B 533
25
CC7
SOFTWARE
ASN B:118 , SER B:120 , HIS B:177 , ASN B:323 , HOH B:911 , HOH B:921
BINDING SITE FOR RESIDUE NAG B 534
[
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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
(2, 4)
Info
All PROSITE Patterns/Profiles
1: GMC_OXRED_1 (A:100-123,B:100-123)
2: GMC_OXRED_2 (A:258-272,B:258-272)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
GMC_OXRED_1
PS00623
GMC oxidoreductases signature 1.
MDL2_PRUDU
127-150
2
A:100-123
B:100-123
2
GMC_OXRED_2
PS00624
GMC oxidoreductases signature 2.
MDL2_PRUDU
285-299
2
A:258-272
B:258-272
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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)
Info
All SCOP Domains
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Sorry, no Info available
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_3gdpA01 (A:9-146,A:192-297,A:367-389,A:457-521)
1b: CATH_3gdpB01 (B:9-146,B:192-297,B:367-389,B:457-521)
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Classes
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Topologies
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(
)
Homologous Superfamilies
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(bba) Sandwich
(528)
Topology
:
FAD/NAD(P)-binding domain
(373)
Homologous Superfamily
:
[code=3.50.50.60, no name defined]
(373)
Sweet almond (Prunus dulcis)
(2)
1a
3gdpA01
A:9-146,A:192-297,A:367-389,A:457-521
1b
3gdpB01
B:9-146,B:192-297,B:367-389,B:457-521
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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