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...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
3RHQ
Asym. Unit
Info
Asym.Unit (368 KB)
Biol.Unit 1 (360 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF THE C707A MUTANT OF C-TERMINAL DOMAIN OF 10'FORMYLTETRAHYDROFOLATE DEHYDROGENASE IN COMPLEX WITH NADP
Authors
:
Y. Tsybovsky
Date
:
12 Apr 11 (Deposition) - 04 May 11 (Release) - 31 Aug 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Fdh, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Tsybovsky, S. A. Krupenko
Conserved Catalytic Residues Of The Aldh1L1 Aldehyde Dehydrogenase Domain Control Binding And Discharging Of The Coenzyme.
J. Biol. Chem. V. 286 23357 2011
[
close entry info
]
Hetero Components
(3, 36)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
2a: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPa)
2b: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPb)
2c: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPc)
2d: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPd)
3a: SULFATE ION (SO4a)
3aa: SULFATE ION (SO4aa)
3ab: SULFATE ION (SO4ab)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
3f: SULFATE ION (SO4f)
3g: SULFATE ION (SO4g)
3h: SULFATE ION (SO4h)
3i: SULFATE ION (SO4i)
3j: SULFATE ION (SO4j)
3k: SULFATE ION (SO4k)
3l: SULFATE ION (SO4l)
3m: SULFATE ION (SO4m)
3n: SULFATE ION (SO4n)
3o: SULFATE ION (SO4o)
3p: SULFATE ION (SO4p)
3q: SULFATE ION (SO4q)
3r: SULFATE ION (SO4r)
3s: SULFATE ION (SO4s)
3t: SULFATE ION (SO4t)
3u: SULFATE ION (SO4u)
3v: SULFATE ION (SO4v)
3w: SULFATE ION (SO4w)
3x: SULFATE ION (SO4x)
3y: SULFATE ION (SO4y)
3z: SULFATE ION (SO4z)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
4
Ligand/Ion
GLYCEROL
2
NAP
4
Ligand/Ion
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
3
SO4
28
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(36, 36)
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)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
VAL A:570 , ILE A:571 , PRO A:572 , TRP A:573 , ASN A:574 , LYS A:597 , ALA A:599 , GLN A:600 , SER A:629 , GLY A:630 , GLY A:634 , GLN A:635 , PHE A:648 , THR A:649 , GLY A:650 , SER A:651 , VAL A:654 , HIS A:657 , ILE A:658 , GLU A:673 , LEU A:674 , GLY A:675 , ALA A:707 , GLU A:804 , PHE A:806 , LEU A:834 , PHE A:872 , HOH A:918 , HOH A:935 , HOH A:950 , HOH A:992 , HOH A:1123 , HOH A:1139 , HOH A:1182 , HOH A:1394 , HOH A:1444 , HOH A:1588
BINDING SITE FOR RESIDUE NAP A 903
02
AC2
SOFTWARE
ASP A:851 , LYS A:852 , ARG C:554
BINDING SITE FOR RESIDUE SO4 A 1
03
AC3
SOFTWARE
HOH A:287 , ARG A:554 , LYS C:852
BINDING SITE FOR RESIDUE SO4 A 2
04
AC4
SOFTWARE
ARG A:636 , PRO A:641 , HOH A:1483 , HOH A:1521
BINDING SITE FOR RESIDUE SO4 A 6
05
AC5
SOFTWARE
ARG A:764 , TYR A:799 , HOH A:1966
BINDING SITE FOR RESIDUE SO4 A 11
06
AC6
SOFTWARE
HOH A:57 , LYS A:669 , LEU A:893 , ARG A:894 , ILE A:895 , HOH A:970 , HOH A:1235 , HOH A:1867 , GLY B:881 , LYS B:882
BINDING SITE FOR RESIDUE SO4 A 15
07
AC7
SOFTWARE
ARG A:551 , ARG A:554 , HOH A:1835 , TYR C:848
BINDING SITE FOR RESIDUE SO4 A 18
08
AC8
SOFTWARE
ASN A:548 , HOH A:1035 , HOH A:1271 , GLN B:528
BINDING SITE FOR RESIDUE SO4 A 21
09
AC9
SOFTWARE
THR A:445 , ASN A:738 , GLU A:741 , ARG A:781 , HOH A:994 , HOH A:1533 , HOH C:1087
BINDING SITE FOR RESIDUE SO4 A 24
10
BC1
SOFTWARE
TYR A:575 , ASN A:706 , THR A:866 , HOH A:1922 , HOH A:2000
BINDING SITE FOR RESIDUE GOL A 29
11
BC2
SOFTWARE
HOH B:255 , HOH B:328 , VAL B:570 , ILE B:571 , PRO B:572 , TRP B:573 , ASN B:574 , LYS B:597 , ALA B:599 , GLN B:600 , SER B:629 , GLY B:630 , GLY B:634 , GLN B:635 , PHE B:648 , THR B:649 , GLY B:650 , SER B:651 , VAL B:654 , HIS B:657 , ILE B:658 , GLU B:673 , LEU B:674 , GLY B:675 , ALA B:707 , GLU B:804 , PHE B:806 , LEU B:834 , PHE B:872 , HOH B:977 , HOH B:984 , HOH B:1010 , HOH B:1186 , HOH B:1202 , HOH B:1297 , HOH B:1443 , HOH B:1684 , HOH B:1707
BINDING SITE FOR RESIDUE NAP B 903
12
BC3
SOFTWARE
ARG B:554 , HOH B:1739 , ASP D:851 , LYS D:852 , HOH D:991
BINDING SITE FOR RESIDUE SO4 B 3
13
BC4
SOFTWARE
LYS B:852 , HOH B:957 , HOH B:1726 , ARG D:554
BINDING SITE FOR RESIDUE SO4 B 4
14
BC5
SOFTWARE
ARG B:636 , PRO B:641
BINDING SITE FOR RESIDUE SO4 B 5
15
BC6
SOFTWARE
ARG B:764 , HOH B:1920
BINDING SITE FOR RESIDUE SO4 B 9
16
BC7
SOFTWARE
HOH A:39 , GLY A:881 , LYS A:882 , HOH B:254 , LYS B:669 , ARG B:894 , ILE B:895 , HOH B:1389
BINDING SITE FOR RESIDUE SO4 B 14
17
BC8
SOFTWARE
ARG B:551 , ARG B:554 , HOH B:1423 , HOH B:1747 , TYR D:848
BINDING SITE FOR RESIDUE SO4 B 19
18
BC9
SOFTWARE
GLN A:528 , ASN B:548 , HOH B:936 , HOH B:979 , HOH B:1097
BINDING SITE FOR RESIDUE SO4 B 22
19
CC1
SOFTWARE
THR B:445 , ASN B:738 , GLU B:741 , ARG B:781 , HOH B:973 , HOH B:1708
BINDING SITE FOR RESIDUE SO4 B 25
20
CC2
SOFTWARE
TYR B:575 , ASN B:706 , THR B:866 , HOH B:2001
BINDING SITE FOR RESIDUE GOL B 30
21
CC3
SOFTWARE
HOH C:200 , HOH C:244 , HOH C:311 , HOH C:332 , VAL C:570 , ILE C:571 , PRO C:572 , TRP C:573 , ASN C:574 , LYS C:597 , ALA C:599 , GLN C:600 , SER C:629 , GLY C:630 , GLY C:634 , GLN C:635 , PHE C:648 , THR C:649 , GLY C:650 , SER C:651 , VAL C:654 , HIS C:657 , ILE C:658 , GLU C:673 , LEU C:674 , GLY C:675 , ALA C:707 , GLU C:804 , PHE C:806 , LEU C:834 , PHE C:872 , HOH C:936 , HOH C:946 , HOH C:1020 , HOH C:1114 , HOH C:1408 , HOH C:1505 , HOH C:1589 , HOH C:1953
BINDING SITE FOR RESIDUE NAP C 903
22
CC4
SOFTWARE
ARG C:636 , PRO C:641 , HOH C:1499 , HOH C:1810
BINDING SITE FOR RESIDUE SO4 C 7
23
CC5
SOFTWARE
ARG C:764 , HOH C:1913
BINDING SITE FOR RESIDUE SO4 C 10
24
CC6
SOFTWARE
HOH C:45 , HOH C:280 , LYS C:669 , ARG C:894 , ILE C:895 , HOH C:942 , HOH C:1066 , GLY D:881 , LYS D:882
BINDING SITE FOR RESIDUE SO4 C 13
25
CC7
SOFTWARE
ARG C:551 , ARG C:554 , HOH C:1813
BINDING SITE FOR RESIDUE SO4 C 17
26
CC8
SOFTWARE
ASN C:548 , HOH C:1043 , HOH C:1049 , HOH C:1085 , HOH C:1842 , LYS D:520 , GLN D:528
BINDING SITE FOR RESIDUE SO4 C 23
27
CC9
SOFTWARE
HOH C:130 , ASN C:738 , ARG C:781
BINDING SITE FOR RESIDUE SO4 C 26
28
DC1
SOFTWARE
LEU A:416 , THR A:417 , LYS C:415 , ARG C:742 , HOH C:1968
BINDING SITE FOR RESIDUE SO4 C 28
29
DC2
SOFTWARE
TYR C:575 , ASN C:706 , THR C:866 , HOH C:2002
BINDING SITE FOR RESIDUE GOL C 31
30
DC3
SOFTWARE
HOH D:161 , HOH D:228 , HOH D:369 , VAL D:570 , ILE D:571 , PRO D:572 , TRP D:573 , ASN D:574 , LYS D:597 , ALA D:599 , GLN D:600 , SER D:629 , GLY D:630 , GLY D:634 , GLN D:635 , PHE D:648 , THR D:649 , GLY D:650 , SER D:651 , VAL D:654 , HIS D:657 , ILE D:658 , GLU D:673 , LEU D:674 , GLY D:675 , ALA D:707 , GLU D:804 , PHE D:806 , LEU D:834 , PHE D:872 , HOH D:948 , HOH D:1007 , HOH D:1213 , HOH D:1216 , HOH D:1322 , HOH D:1345 , HOH D:1662
BINDING SITE FOR RESIDUE NAP D 903
31
DC4
SOFTWARE
ARG D:636 , PRO D:641 , HOH D:1959
BINDING SITE FOR RESIDUE SO4 D 8
32
DC5
SOFTWARE
ARG D:764
BINDING SITE FOR RESIDUE SO4 D 12
33
DC6
SOFTWARE
GLY C:881 , LYS C:882 , HOH C:1851 , HOH D:53 , LYS D:669 , LEU D:893 , ARG D:894 , ILE D:895 , HOH D:905 , HOH D:1037 , HOH D:1198
BINDING SITE FOR RESIDUE SO4 D 16
34
DC7
SOFTWARE
TYR B:848 , ARG D:551 , ARG D:554
BINDING SITE FOR RESIDUE SO4 D 20
35
DC8
SOFTWARE
THR D:445 , ASN D:738 , GLU D:741 , ARG D:781 , HOH D:983 , HOH D:1575
BINDING SITE FOR RESIDUE SO4 D 27
36
DC9
SOFTWARE
TYR D:575 , MET D:578 , TRP D:582 , ASN D:706 , THR D:866 , HOH D:1352 , HOH D:2003
BINDING SITE FOR RESIDUE GOL D 32
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: ALDEHYDE_DEHYDR_GLU (A:672-679,B:672-679,C:672-679,D:67...)
2: ALDEHYDE_DEHYDR_CYS (A:700-711,B:700-711,C:700-711,D:70...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ALDEHYDE_DEHYDR_GLU
PS00687
Aldehyde dehydrogenases glutamic acid active site.
AL1L1_RAT
672-679
4
A:672-679
B:672-679
C:672-679
D:672-679
2
ALDEHYDE_DEHYDR_CYS
PS00070
Aldehyde dehydrogenases cysteine active site.
AL1L1_RAT
700-711
4
A:700-711
B:700-711
C:700-711
D:700-711
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d3rhqa_ (A:)
1b: SCOP_d3rhqb_ (B:)
1c: SCOP_d3rhqc_ (C:)
1d: SCOP_d3rhqd_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
ALDH-like
(168)
Superfamily
:
ALDH-like
(168)
Family
:
automated matches
(88)
Protein domain
:
automated matches
(88)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(12)
1a
d3rhqa_
A:
1b
d3rhqb_
B:
1c
d3rhqc_
C:
1d
d3rhqd_
D:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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
Chain B
Chain C
Chain D
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 (368 KB)
Header - Asym.Unit
Biol.Unit 1 (360 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
3RHQ
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help