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3GDN
Asym. Unit
Info
Asym.Unit (204 KB)
Biol.Unit 1 (101 KB)
Biol.Unit 2 (101 KB)
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(1)
Title
:
ALMOND HYDROXYNITRILE LYASE IN COMPLEX WITH BENZALDEHYDE
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
:
1.67
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
(for further references see the
PDB file header
)
[
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Hetero Components
(7, 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: BENZALDEHYDE (HBXa)
4b: BENZALDEHYDE (HBXb)
5a: ALPHA-D-MANNOSE (MANa)
5b: ALPHA-D-MANNOSE (MANb)
5c: ALPHA-D-MANNOSE (MANc)
6a: (2R)-HYDROXY(PHENYL)ETHANENITRILE (MXNa)
6b: (2R)-HYDROXY(PHENYL)ETHANENITRILE (MXNb)
6c: (2R)-HYDROXY(PHENYL)ETHANENITRILE (MXNc)
6d: (2R)-HYDROXY(PHENYL)ETHANENITRILE (MXNd)
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)
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
HBX
2
Ligand/Ion
BENZALDEHYDE
5
MAN
3
Ligand/Ion
ALPHA-D-MANNOSE
6
MXN
4
Ligand/Ion
(2R)-HYDROXY(PHENYL)ETHANENITRILE
7
NAG
10
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
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
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:535 , HOH A:553 , HOH A:571 , HOH A:600 , HOH A:618 , HOH A:625 , HOH A:632 , HOH A:1025
BINDING SITE FOR RESIDUE FAD A 522
02
AC2
SOFTWARE
ASN A:118 , HIS A:177 , ASN A:323 , HOH A:684 , HOH A:956 , HOH A:1023 , HOH A:1062
BINDING SITE FOR RESIDUE NAG A 523
03
AC3
SOFTWARE
ARG A:116 , ASP A:132 , ASN A:135 , ASP A:176 , NAG A:525 , HOH A:637 , HOH A:757 , HOH A:794 , HOH A:1047
BINDING SITE FOR RESIDUE NAG A 524
04
AC4
SOFTWARE
THR A:119 , GLU A:178 , NAG A:524 , MAN A:526 , HOH A:716
BINDING SITE FOR RESIDUE NAG A 525
05
AC5
SOFTWARE
NAG A:525 , HOH A:1267
BINDING SITE FOR RESIDUE MAN A 526
06
AC6
SOFTWARE
LEU A:366 , SER A:391 , ASN A:392 , NAG A:528 , FUC A:529 , HOH A:671 , HOH A:731
BINDING SITE FOR RESIDUE NAG A 527
07
AC7
SOFTWARE
NAG A:527 , FUC A:529 , HOH A:1111
BINDING SITE FOR RESIDUE NAG A 528
08
AC8
SOFTWARE
NAG A:527 , NAG A:528
BINDING SITE FOR RESIDUE FUC A 529
09
AC9
SOFTWARE
ALA A:111 , CYS A:328 , PHE A:330 , HIS A:357 , TYR A:457 , HIS A:497
BINDING SITE FOR RESIDUE HBX A 530
10
BC1
SOFTWARE
ILE A:121 , SER A:125 , PHE A:490 , PRO A:491 , TYR A:492 , PHE A:501 , HOH A:820 , HOH A:1023
BINDING SITE FOR RESIDUE MXN A 531
11
BC2
SOFTWARE
LYS A:148 , PRO A:149 , LYS A:159 , GLY A:172 , PHE A:173 , ILE A:183
BINDING SITE FOR RESIDUE MXN A 532
12
BC3
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:548 , HOH B:555 , HOH B:574 , HOH B:587 , HOH B:589 , HOH B:616 , HOH B:651 , HOH B:973
BINDING SITE FOR RESIDUE FAD B 522
13
BC4
SOFTWARE
NAG B:524 , FUC B:525 , BMA B:526 , HOH B:1041
BINDING SITE FOR RESIDUE NAG B 523
14
BC5
SOFTWARE
LEU B:366 , ASN B:392 , NAG B:523 , FUC B:525 , HOH B:684 , HOH B:722 , HOH B:824
BINDING SITE FOR RESIDUE NAG B 524
15
BC6
SOFTWARE
NAG B:523 , NAG B:524
BINDING SITE FOR RESIDUE FUC B 525
16
BC7
SOFTWARE
ASP A:422 , NAG B:523 , MAN B:527 , HOH B:1336
BINDING SITE FOR RESIDUE BMA B 526
17
BC8
SOFTWARE
LYS A:416 , PRO A:417 , ASP A:422 , HOH A:949 , HOH A:1359 , BMA B:526 , HOH B:819 , HOH B:1239 , HOH B:1336
BINDING SITE FOR RESIDUE MAN B 527
18
BC9
SOFTWARE
ARG B:116 , ASP B:132 , ASN B:135 , ASP B:176 , NAG B:529 , HOH B:638 , HOH B:815 , HOH B:1393
BINDING SITE FOR RESIDUE NAG B 528
19
CC1
SOFTWARE
GLU B:178 , NAG B:528 , BMA B:530 , HOH B:1274
BINDING SITE FOR RESIDUE NAG B 529
20
CC2
SOFTWARE
NAG B:529 , MAN B:531
BINDING SITE FOR RESIDUE BMA B 530
21
CC3
SOFTWARE
HIS B:171 , GLU B:178 , BMA B:530 , HOH B:545 , HOH B:762 , HOH B:981 , HOH B:992
BINDING SITE FOR RESIDUE MAN B 531
22
CC4
SOFTWARE
ASN B:118 , SER B:120 , ILE B:121 , HIS B:177 , ASN B:323 , HOH B:641 , HOH B:695 , HOH B:966 , HOH B:1343
BINDING SITE FOR RESIDUE NAG B 532
23
CC5
SOFTWARE
CYS B:328 , PHE B:330 , HIS B:357 , TYR B:457 , HIS B:497
BINDING SITE FOR RESIDUE HBX B 533
24
CC6
SOFTWARE
ILE B:121 , SER B:125 , PHE B:490 , PRO B:491 , TYR B:492 , PHE B:501 , HOH B:541 , HOH B:966
BINDING SITE FOR RESIDUE MXN B 534
25
CC7
SOFTWARE
LYS B:148 , PRO B:149 , LYS B:159 , GLY B:172 , ILE B:183
BINDING SITE FOR RESIDUE MXN B 535
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
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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:
Select:
Label:
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_3gdnA01 (A:9-146,A:192-297,A:367-389,A:457-521)
1b: CATH_3gdnB01 (B:9-146,B:192-297,B:367-389,B:457-521)
View:
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Classes
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(
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(
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Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
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
3gdnA01
A:9-146,A:192-297,A:367-389,A:457-521
1b
3gdnB01
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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