PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
1HDR
Asym. Unit
Info
Asym.Unit (43 KB)
Biol.Unit 1 (76 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
THE CRYSTALLOGRAPHIC STRUCTURE OF A HUMAN DIHYDROPTERIDINE REDUCTASE NADH BINARY COMPLEX EXPRESSED IN ESCHERICHIA COLI BY A CDNA CONSTRUCTED FROM ITS RAT HOMOLOGUE
Authors
:
K. I. Varughese, Y. Su, N. H. Xuong, J. M. Whiteley
Date
:
18 Aug 93 (Deposition) - 31 Aug 94 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Keywords
:
Oxidoreductase(Acting On Nadh)
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Su, K. I. Varughese, N. H. Xuong, T. L. Bray, D. J. Roche, J. M. Whitele
The Crystallographic Structure Of A Human Dihydropteridine Reductase Nadh Binary Complex Expressed In Escherichia Coli By A Cdna Constructed From Its Rat Homologue.
J. Biol. Chem. V. 268 26836 1993
[
close entry info
]
Hetero Components
(1, 1)
Info
All Hetero Components
1a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAD
1
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
[
close Hetero Component info
]
Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
TYR A:15 , GLY A:16 , ARG A:18 , GLY A:19 , ALA A:20 , LEU A:21 , VAL A:39 , ASP A:40 , VAL A:53 , LYS A:72 , VAL A:85 , ALA A:86 , GLY A:87 , GLY A:88 , THR A:113 , ALA A:134 , TYR A:149 , LYS A:153 , PRO A:181 , VAL A:182 , THR A:183 , LEU A:184 , ASN A:189 , HOH A:247 , HOH A:249 , HOH A:252
BINDING SITE FOR RESIDUE NAD A 244
[
close Site info
]
SAPs(SNPs)/Variants
(17, 17)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_008121 (L13P, chain A, )
02: VAR_021767 (G16R, chain A, )
03: VAR_008122 (G16V, chain A, )
04: VAR_021768 (G17D, chain A, )
05: VAR_006960 (G22D, chain A, )
06: VAR_006961 (W35R, chain A, )
07: VAR_013027 (S50T, chain A, )
08: VAR_021769 (Q65R, chain A, )
09: VAR_006962 (L73P, chain A, )
10: VAR_006963 (W107G, chain A, )
11: VAR_006965 (P144L, chain A, )
12: VAR_021770 (G148R, chain A, )
13: VAR_006966 (Y149C, chain A, )
14: VAR_006967 (G150S, chain A, )
15: VAR_006968 (H157Y, chain A, )
16: VAR_006969 (G169S, chain A, )
17: VAR_006970 (F211C, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_008121
L
14
P
DHPR_HUMAN
Disease (HPABH4C)
---
A
L
13
P
02
UniProt
VAR_021767
G
17
R
DHPR_HUMAN
Disease (HPABH4C)
---
A
G
16
R
03
UniProt
VAR_008122
G
17
V
DHPR_HUMAN
Disease (HPABH4C)
---
A
G
16
V
04
UniProt
VAR_021768
G
18
D
DHPR_HUMAN
Disease (HPABH4C)
---
A
G
17
D
05
UniProt
VAR_006960
G
23
D
DHPR_HUMAN
Disease (HPABH4C)
---
A
G
22
D
06
UniProt
VAR_006961
W
36
R
DHPR_HUMAN
Disease (HPABH4C)
---
A
W
35
R
07
UniProt
VAR_013027
S
51
T
DHPR_HUMAN
Polymorphism
---
A
S
50
T
08
UniProt
VAR_021769
Q
66
R
DHPR_HUMAN
Disease (HPABH4C)
---
A
Q
65
R
09
UniProt
VAR_006962
L
74
P
DHPR_HUMAN
Disease (HPABH4C)
---
A
L
73
P
10
UniProt
VAR_006963
W
108
G
DHPR_HUMAN
Disease (HPABH4C)
---
A
W
107
G
11
UniProt
VAR_006965
P
145
L
DHPR_HUMAN
Disease (HPABH4C)
---
A
P
144
L
12
UniProt
VAR_021770
G
149
R
DHPR_HUMAN
Disease (HPABH4C)
---
A
G
148
R
13
UniProt
VAR_006966
Y
150
C
DHPR_HUMAN
Disease (HPABH4C)
---
A
Y
149
C
14
UniProt
VAR_006967
G
151
S
DHPR_HUMAN
Disease (HPABH4C)
---
A
G
150
S
15
UniProt
VAR_006968
H
158
Y
DHPR_HUMAN
Disease (HPABH4C)
---
A
H
157
Y
16
UniProt
VAR_006969
G
170
S
DHPR_HUMAN
Disease (HPABH4C)
---
A
G
169
S
17
UniProt
VAR_006970
F
212
C
DHPR_HUMAN
Disease (HPABH4C)
---
A
F
211
C
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: ADH_SHORT (A:136-164)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ADH_SHORT
PS00061
Short-chain dehydrogenases/reductases family signature.
DHPR_HUMAN
137-165
1
A:136-164
[
close PROSITE info
]
Exons
(7, 7)
Info
All Exons
Exon 1.1a (A:8-34)
Exon 1.3 (A:35-65)
Exon 1.4 (A:66-98)
Exon 1.5 (A:98-145)
Exon 1.6c (A:145-181)
Exon 1.7a (A:181-209)
Exon 1.8f (A:209-243)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1a
2: Boundary 1.1a/1.3
3: Boundary 1.3/1.4
4: Boundary 1.4/1.5
5: Boundary 1.5/1.6c
6: Boundary 1.6c/1.7a
7: Boundary 1.7a/1.8f
8: Boundary 1.8f/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1a
ENST00000281243
1a
ENSE00001693584
chr4:
17513857-17513573
285
DHPR_HUMAN
1-35
35
1
A:8-34
27
1.3
ENST00000281243
3
ENSE00001133183
chr4:
17510986-17510894
93
DHPR_HUMAN
36-66
31
1
A:35-65
31
1.4
ENST00000281243
4
ENSE00001133173
chr4:
17506098-17506002
97
DHPR_HUMAN
67-99
33
1
A:66-98
33
1.5
ENST00000281243
5
ENSE00001000268
chr4:
17503482-17503342
141
DHPR_HUMAN
99-146
48
1
A:98-145
48
1.6c
ENST00000281243
6c
ENSE00001133162
chr4:
17493963-17493855
109
DHPR_HUMAN
146-182
37
1
A:145-181
37
1.7a
ENST00000281243
7a
ENSE00001133153
chr4:
17492368-17492285
84
DHPR_HUMAN
182-210
29
1
A:181-209
29
1.8f
ENST00000281243
8f
ENSE00001000269
chr4:
17488859-17488021
839
DHPR_HUMAN
210-244
35
1
A:209-243
35
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d1hdra_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
Tyrosine-dependent oxidoreductases
(503)
Protein domain
:
Dihydropteridin reductase (pteridine reductase)
(24)
Human (Homo sapiens) [TaxId: 9606]
(1)
1a
d1hdra_
A:
[
close SCOP info
]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_1hdrA00 (A:8-243)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Human (Homo sapiens)
(188)
1a
1hdrA00
A:8-243
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (43 KB)
Header - Asym.Unit
Biol.Unit 1 (76 KB)
Header - Biol.Unit 1
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
1HDR
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
