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.
2PLA
Asym. Unit
Info
Asym.Unit (116 KB)
Biol.Unit 1 (109 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 HUMAN GLYCEROL-3-PHOSPHATE DEHYDROGENASE 1-LIKE PROTEIN
Authors
:
J. Uppenberg, C. Smee, V. Hozjan, K. Kavanagh, G. Bunkoczi, E. Papagrig A. C. W. Pike, E. Ugochukwu, C. Umeano, F. Von Delft, J. Weigelt, C. H. Arrowsmith, A. Edwards, M. Sundstrom, U. Oppermann, Structural Consortium (Sgc)
Date
:
19 Apr 07 (Deposition) - 01 May 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.51
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Dehydrogenase, Structural Genomics, Structural Genomics Consortium, Sgc, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Uppenberg, C. Smee, V. Hozjan, K. Kavanagh, G. Bunkoczi, E. Papagrigoriou, A. C. W. Pike, E. Ugochukwu, C. Umeano, F. Von Delft J. Weigelt, C. H. Arrowsmith, A. Edwards, M. Sundstrom, U. Oppermann
Crystal Structure Of Human Glycerol-3-Phosphate Dehydrogenase 1-Like Protein.
To Be Published
[
close entry info
]
Hetero Components
(3, 6)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
2a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
2b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
3a: PHOSPHATE ION (PO4a)
3b: PHOSPHATE ION (PO4b)
3c: PHOSPHATE ION (PO4c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
1
Ligand/Ion
CHLORIDE ION
2
NAD
2
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
3
PO4
3
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LYS A:206 , ASN A:207 , THR A:266 , GLY A:270 , ARG A:271 , ASN A:272 , HOH A:507 , HOH A:566
BINDING SITE FOR RESIDUE PO4 A 501
2
AC2
SOFTWARE
LYS B:206 , ASN B:207 , THR B:266 , GLY B:270 , ARG B:271 , ASN B:272 , HOH B:602 , HOH B:604 , HOH B:610 , HOH B:643
BINDING SITE FOR RESIDUE PO4 B 502
3
AC3
SOFTWARE
LYS A:22 , HIS A:69 , LYS A:70 , LYS A:320
BINDING SITE FOR RESIDUE PO4 A 503
4
AC4
SOFTWARE
LYS B:22 , LYS B:70
BINDING SITE FOR RESIDUE CL B 601
5
AC5
SOFTWARE
GLY A:14 , ASN A:15 , TRP A:16 , GLY A:17 , PHE A:43 , TYR A:65 , PHE A:99 , ARG A:102 , ILE A:121 , LYS A:122 , ASN A:153 , ALA A:155 , ARG A:271 , GLY A:296 , GLN A:297 , LYS A:298 , HOH A:506 , HOH A:566 , HOH A:567 , HOH A:574 , HOH A:575 , HOH A:576 , HOH A:582 , HOH A:588
BINDING SITE FOR RESIDUE NAD A 401
6
AC6
SOFTWARE
GLY B:14 , ASN B:15 , TRP B:16 , GLY B:17 , PHE B:43 , TYR B:65 , VAL B:94 , PRO B:96 , PHE B:99 , LEU B:120 , ILE B:121 , LYS B:122 , ASN B:153 , ILE B:154 , ALA B:155 , ARG B:271 , GLY B:296 , GLN B:297 , LYS B:298 , GLN B:300 , HOH B:604 , HOH B:610 , HOH B:619 , HOH B:643
BINDING SITE FOR RESIDUE NAD B 401
[
close Site info
]
SAPs(SNPs)/Variants
(5, 10)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_044044 (E83K, chain A/B, )
2: VAR_044045 (I124V, chain A/B, )
3: VAR_032114 (L178F, chain A/B, )
4: VAR_044046 (R273C, chain A/B, )
5: VAR_044047 (A280V, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_044044
E
83
K
GPD1L_HUMAN
Disease (SIDS)
---
A/B
E
83
K
2
UniProt
VAR_044045
I
124
V
GPD1L_HUMAN
Disease (SIDS)
72552293
A/B
I
124
V
3
UniProt
VAR_032114
L
178
F
GPD1L_HUMAN
Polymorphism
35447795
A/B
L
178
F
4
UniProt
VAR_044046
R
273
C
GPD1L_HUMAN
Disease (SIDS)
---
A/B
R
273
C
5
UniProt
VAR_044047
A
280
V
GPD1L_HUMAN
Disease (BRGDA2)
---
A/B
A
280
V
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(8, 16)
Info
All Exons
Exon 1.2a (A:4-16 | B:4-16)
Exon 1.3 (A:16-75 | B:16-75)
Exon 1.4 (A:76-122 | B:76-122)
Exon 1.5b (A:123-169 | B:123-169)
Exon 1.6b (A:169-206 | B:169-206)
Exon 1.7d (A:207-284 | B:207-284)
Exon 1.8b (A:285-320 | B:285-320)
Exon 1.9c (A:320-346 | B:320-346)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.2a
2: Boundary 1.2a/1.3
3: Boundary 1.3/1.4
4: Boundary 1.4/1.5b
5: Boundary 1.5b/1.6b
6: Boundary 1.6b/1.7d
7: Boundary 1.7d/1.8b
8: Boundary 1.8b/1.9c
9: Boundary 1.9c/-
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
1.2a
ENST00000282541
2a
ENSE00001134616
chr3:
32148003-32148250
248
GPD1L_HUMAN
1-16
16
2
A:4-16
B:4-16
13
13
1.3
ENST00000282541
3
ENSE00001721944
chr3:
32169568-32169745
178
GPD1L_HUMAN
16-75
60
2
A:16-75
B:16-75
60
60
1.4
ENST00000282541
4
ENSE00001635877
chr3:
32180079-32180219
141
GPD1L_HUMAN
76-122
47
2
A:76-122
B:76-122
47
47
1.5b
ENST00000282541
5b
ENSE00001650240
chr3:
32181720-32181858
139
GPD1L_HUMAN
123-169
47
2
A:123-169
B:123-169
47
47
1.6b
ENST00000282541
6b
ENSE00001777860
chr3:
32188114-32188226
113
GPD1L_HUMAN
169-206
38
2
A:169-206
B:169-206
38
38
1.7d
ENST00000282541
7d
ENSE00001665323
chr3:
32200368-32200601
234
GPD1L_HUMAN
207-284
78
2
A:207-284
B:207-284
78
78
1.8b
ENST00000282541
8b
ENSE00001075713
chr3:
32201060-32201166
107
GPD1L_HUMAN
285-320
36
2
A:285-320
B:285-320
36
36
1.9c
ENST00000282541
9c
ENSE00001134607
chr3:
32207306-32210205
2900
GPD1L_HUMAN
320-351
32
2
A:320-346
B:320-346
27
27
[
close EXON info
]
SCOP Domains
(2, 3)
Info
All SCOP Domains
1a: SCOP_d2plaa2 (A:196-346)
2a: SCOP_d2plaa1 (A:4-195)
2b: SCOP_d2plab1 (B:4-195)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
6-phosphogluconate dehydrogenase C-terminal domain-like
(119)
Superfamily
:
6-phosphogluconate dehydrogenase C-terminal domain-like
(119)
Family
:
automated matches
(50)
Protein domain
:
automated matches
(50)
Human (Homo sapiens) [TaxId: 9606]
(13)
1a
d2plaa2
A:196-346
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
:
automated matches
(447)
Protein domain
:
automated matches
(447)
Human (Homo sapiens) [TaxId: 9606]
(32)
2a
d2plaa1
A:4-195
2b
d2plab1
B:4-195
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_NAD_Gly3P_dh_C_2plaB01 (B:194-344)
1b: PFAM_NAD_Gly3P_dh_C_2plaB02 (B:194-344)
2a: PFAM_NAD_Gly3P_dh_N_2plaB03 (B:7-176)
2b: PFAM_NAD_Gly3P_dh_N_2plaB04 (B:7-176)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
6PGD_C
(47)
Family
:
NAD_Gly3P_dh_C
(11)
Homo sapiens (Human)
(4)
1a
NAD_Gly3P_dh_C-2plaB01
B:194-344
1b
NAD_Gly3P_dh_C-2plaB02
B:194-344
Clan
:
NADP_Rossmann
(1239)
Family
:
NAD_Gly3P_dh_N
(11)
Homo sapiens (Human)
(4)
2a
NAD_Gly3P_dh_N-2plaB03
B:7-176
2b
NAD_Gly3P_dh_N-2plaB04
B:7-176
[
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
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 (116 KB)
Header - Asym.Unit
Biol.Unit 1 (109 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
2PLA
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
