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1BW9
Asym. Unit
Info
Asym.Unit (133 KB)
Biol.Unit 1 (127 KB)
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(1)
Title
:
PHENYLALANINE DEHYDROGENASE STRUCTURE IN TERNARY COMPLEX WITH NAD+ AND PHENYLPYRUVATE
Authors
:
J. L. Vanhooke, J. B. Thoden, N. M. W. Brunhuber, J. L. Blanchard, H. M. Holden
Date
:
01 Oct 98 (Deposition) - 18 May 99 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.50
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Amino Acid Dehydrogenase, Oxidative Deamination Mechanism
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. L. Vanhooke, J. B. Thoden, N. M. Brunhuber, J. S. Blanchard, H. M. Holden
Phenylalanine Dehydrogenase From Rhodococcus Sp. M4: High-Resolution X-Ray Analyses Of Inhibitory Ternary Complexes Reveal Key Features In The Oxidative Deamination Mechanism.
Biochemistry V. 38 2326 1999
(for further references see the
PDB file header
)
[
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Hetero Components
(7, 16)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
2a: ISOPROPYL ALCOHOL (IPAa)
2b: ISOPROPYL ALCOHOL (IPAb)
2c: ISOPROPYL ALCOHOL (IPAc)
2d: ISOPROPYL ALCOHOL (IPAd)
3a: POTASSIUM ION (Ka)
3b: POTASSIUM ION (Kb)
5a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
5b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
6a: PHOSPHATE ION (PO4a)
7a: 3-PHENYLPYRUVIC ACID (PPYa)
7b: 3-PHENYLPYRUVIC ACID (PPYb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
3
Ligand/Ion
1,2-ETHANEDIOL
2
IPA
4
Ligand/Ion
ISOPROPYL ALCOHOL
3
K
2
Ligand/Ion
POTASSIUM ION
4
NA
2
Ligand/Ion
SODIUM ION
5
NAD
2
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
6
PO4
1
Ligand/Ion
PHOSPHATE ION
7
PPY
2
Ligand/Ion
3-PHENYLPYRUVIC ACID
[
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Sites
(16, 16)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:118 , THR A:121 , HOH A:656 , HOH A:728 , HOH B:884
BINDING SITE FOR RESIDUE K B 850
02
AC2
SOFTWARE
HOH A:371 , HOH A:436 , ASP B:409 , HOH B:1100 , HOH B:1227 , HOH B:1319
BINDING SITE FOR RESIDUE NA B 851
03
AC3
SOFTWARE
GLN B:600 , GLY B:618 , HOH B:1008 , HOH B:1083 , HOH B:1326
BINDING SITE FOR RESIDUE NA B 852
04
AC4
SOFTWARE
LEU B:570 , SER B:572 , ASP B:574 , LEU B:576 , PO4 B:880 , HOH B:993 , HOH B:1140
BINDING SITE FOR RESIDUE K B 853
05
AC5
SOFTWARE
SER B:401 , SER B:404 , LYS B:458 , LEU B:570 , LEU B:576 , K B:853 , HOH B:1019 , HOH B:1038 , HOH B:1140 , HOH B:1157 , HOH B:1204
BINDING SITE FOR RESIDUE PO4 B 880
06
AC6
SOFTWARE
LYS A:66 , LYS A:78 , PRO A:117 , ASP A:118 , VAL A:119 , GLY A:182 , GLY A:184 , ALA A:185 , VAL A:186 , ALA A:204 , ASP A:205 , THR A:206 , ARG A:210 , LEU A:224 , CYS A:238 , ALA A:239 , MET A:240 , ALA A:260 , ALA A:261 , ASN A:262 , PPY A:361 , HOH A:394 , HOH A:395 , HOH A:446 , HOH A:493 , HOH A:521 , HOH A:552 , HOH A:656 , HOH A:761 , HOH A:771 , EDO B:874 , HOH B:881
BINDING SITE FOR RESIDUE NAD A 360
07
AC7
SOFTWARE
GLY A:39 , GLY A:40 , MET A:63 , LYS A:66 , LYS A:78 , GLY A:116 , PRO A:117 , GLY A:291 , ALA A:292 , LEU A:295 , NAD A:360 , HOH A:414 , HOH B:882
BINDING SITE FOR RESIDUE PPY A 361
08
AC8
SOFTWARE
LEU B:583 , GLY B:584 , ALA B:585 , VAL B:586 , ASP B:605 , THR B:606 , ARG B:610 , HOH B:905 , HOH B:907 , HOH B:935 , HOH B:1044 , HOH B:1239 , HOH B:1381
BINDING SITE FOR RESIDUE NAD B 760
09
AC9
SOFTWARE
HOH A:382 , GLY B:439 , GLY B:440 , MET B:463 , LYS B:466 , LYS B:478 , GLY B:516 , PRO B:517
BINDING SITE FOR RESIDUE PPY B 761
10
BC1
SOFTWARE
MET B:474 , IPA B:861 , HOH B:1193
BINDING SITE FOR RESIDUE EDO B 871
11
BC2
SOFTWARE
HOH A:600 , HOH B:887
BINDING SITE FOR RESIDUE EDO B 873
12
BC3
SOFTWARE
SER A:149 , ALA A:150 , THR A:153 , VAL A:186 , NAD A:360 , HOH B:881 , HOH B:882 , HOH B:884
BINDING SITE FOR RESIDUE EDO B 874
13
BC4
SOFTWARE
CYS A:232 , ASP A:253 , CYS A:254 , SER A:255 , HOH A:610
BINDING SITE FOR RESIDUE IPA B 860
14
BC5
SOFTWARE
ALA A:276 , LEU B:434 , PRO B:473 , EDO B:871 , HOH B:1071
BINDING SITE FOR RESIDUE IPA B 861
15
BC6
SOFTWARE
ARG B:442 , ASP B:455 , LYS B:458 , LEU B:459 , ASN B:663 , HOH B:1123
BINDING SITE FOR RESIDUE IPA B 862
16
BC7
SOFTWARE
THR A:15 , LEU A:49 , LEU B:406 , ARG B:428 , HOH B:985
BINDING SITE FOR RESIDUE IPA B 863
[
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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
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1bw9a2 (A:1-148)
1b: SCOP_d1bw9b2 (B:401-548)
2a: SCOP_d1bw9a1 (A:149-350)
2b: SCOP_d1bw9b1 (B:549-747)
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Aminoacid dehydrogenase-like, N-terminal domain
(100)
Superfamily
:
Aminoacid dehydrogenase-like, N-terminal domain
(100)
Family
:
Aminoacid dehydrogenases
(28)
Protein domain
:
Phenylalanine dehydrogenase
(4)
Rhodococcus sp., M4 [TaxId: 1831]
(4)
1a
d1bw9a2
A:1-148
1b
d1bw9b2
B:401-548
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
Aminoacid dehydrogenase-like, C-terminal domain
(67)
Protein domain
:
Phenylalanine dehydrogenase
(4)
Rhodococcus sp., M4 [TaxId: 1831]
(4)
2a
d1bw9a1
A:149-350
2b
d1bw9b1
B:549-747
[
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1bw9A01 (A:3-64,A:75-136,A:339-350)
1b: CATH_1bw9B01 (B:401-464,B:475-536,B:739-747)
2a: CATH_1bw9A02 (A:137-338)
2b: CATH_1bw9B02 (B:537-738)
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)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Leucine Dehydrogenase; Chain A, domain 1
(52)
Homologous Superfamily
:
Leucine Dehydrogenase, chain A, domain 1
(52)
Rhodococcus sp.. Organism_taxid: 1831. Cell_line: bl21.
(2)
1a
1bw9A01
A:3-64,A:75-136,A:339-350
1b
1bw9B01
B:401-464,B:475-536,B:739-747
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Rhodococcus sp.. Organism_taxid: 1831. Cell_line: bl21.
(2)
2a
1bw9A02
A:137-338
2b
1bw9B02
B:537-738
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Asymmetric Unit 1
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Asym.Unit (133 KB)
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