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.
2G82
Asym. Unit
Info
Asym.Unit (450 KB)
Biol.Unit 1 (226 KB)
Biol.Unit 2 (221 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
HIGH RESOLUTION STRUCTURES OF THERMUS AQUATICUS GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE: ROLE OF 220'S LOOP MOTION IN CATALYSIS
Authors
:
J. L. Jenkins, R. Buencamino, J. J. Tanner
Date
:
01 Mar 06 (Deposition) - 13 Mar 07 (Release) - 12 Nov 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.65
Chains
:
Asym. Unit : A,B,C,D,O,P,Q,R
Biol. Unit 1: O,P,Q,R (1x)
Biol. Unit 2: A,B,C,D (1x)
Keywords
:
Gapdh, G3Pdh, Glycolysis, Oxidoreductase, Nad, Rossmann Fold
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. L. Jenkins, R. Buencamino, J. J. Tanner
High Resolution Structures Of Thermus Aquaticus Glyceraldehyde-3-Phosphate Dehydrogenase: Role Of 220'S Loo Motion In Catalysis
To Be Published
[
close entry info
]
Hetero Components
(6, 23)
Info
All Hetero Components
1a: 3-SULFINOALANINE (CSDa)
1b: 3-SULFINOALANINE (CSDb)
1c: 3-SULFINOALANINE (CSDc)
1d: 3-SULFINOALANINE (CSDd)
1e: 3-SULFINOALANINE (CSDe)
1f: 3-SULFINOALANINE (CSDf)
1g: 3-SULFINOALANINE (CSDg)
1h: 3-SULFINOALANINE (CSDh)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
3a: ISOPROPYL ALCOHOL (IPAa)
3b: ISOPROPYL ALCOHOL (IPAb)
5a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
5b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
5c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
5d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
5e: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADe)
5f: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADf)
5g: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADg)
5h: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADh)
4a: SODIUM ION (NAa)
6a: TRIETHYLENE GLYCOL (PGEa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CSD
8
Mod. Amino Acid
3-SULFINOALANINE
2
GOL
3
Ligand/Ion
GLYCEROL
3
IPA
2
Ligand/Ion
ISOPROPYL ALCOHOL
4
NA
1
Ligand/Ion
SODIUM ION
5
NAD
8
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
6
PGE
1
Ligand/Ion
TRIETHYLENE GLYCOL
[
close Hetero Component info
]
Sites
(15, 15)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PGE C:1700 , HOH C:1853 , HOH C:1996 , HOH Q:3563 , HOH Q:3699
BINDING SITE FOR RESIDUE NA C 1600
02
AC2
SOFTWARE
ASN O:6 , GLY O:7 , GLY O:9 , ARG O:10 , ILE O:11 , ASN O:30 , ASP O:31 , LEU O:32 , LYS O:75 , SER O:93 , THR O:94 , GLY O:95 , PHE O:97 , THR O:117 , ALA O:118 , CSD O:149 , ASN O:180 , ASN O:311 , TYR O:315 , HOH O:341 , HOH O:355 , HOH O:368 , HOH O:377 , HOH O:384 , HOH O:424 , HOH O:431 , HOH O:446 , HOH O:469 , HOH O:479 , HOH O:521 , LEU R:187 , HOH R:3525
BINDING SITE FOR RESIDUE NAD O 336
03
AC3
SOFTWARE
ASN P:6 , GLY P:7 , GLY P:9 , ARG P:10 , ILE P:11 , ASN P:30 , ASP P:31 , LEU P:32 , LYS P:75 , SER P:93 , THR P:94 , GLY P:95 , PHE P:97 , THR P:117 , ALA P:118 , CSD P:149 , ASN P:180 , ASN P:311 , TYR P:315 , HOH P:337 , HOH P:343 , HOH P:351 , HOH P:361 , HOH P:369 , HOH P:396 , HOH P:404 , HOH P:411 , HOH P:417 , HOH P:422 , HOH P:455 , HOH P:476 , LEU Q:187 , HOH Q:3520
BINDING SITE FOR RESIDUE NAD P 336
04
AC4
SOFTWARE
LEU P:187 , HOH P:339 , ASN Q:6 , GLY Q:7 , GLY Q:9 , ARG Q:10 , ILE Q:11 , ASN Q:30 , ASP Q:31 , LEU Q:32 , LYS Q:75 , SER Q:93 , THR Q:94 , GLY Q:95 , PHE Q:97 , THR Q:117 , ALA Q:118 , CSD Q:149 , ASN Q:180 , ASN Q:311 , TYR Q:315 , HOH Q:3504 , HOH Q:3508 , HOH Q:3522 , HOH Q:3541 , HOH Q:3554 , HOH Q:3590 , HOH Q:3601 , HOH Q:3603 , HOH Q:3619 , HOH Q:3631 , HOH Q:3667 , HOH Q:3681 , HOH Q:3688
BINDING SITE FOR RESIDUE NAD Q 336
05
AC5
SOFTWARE
LEU O:187 , HOH O:347 , ASN R:6 , GLY R:7 , GLY R:9 , ARG R:10 , ILE R:11 , ASN R:30 , ASP R:31 , LEU R:32 , LYS R:75 , SER R:93 , THR R:94 , GLY R:95 , PHE R:97 , THR R:117 , ALA R:118 , CSD R:149 , ASN R:180 , ASN R:311 , TYR R:315 , HOH R:3504 , HOH R:3505 , HOH R:3508 , HOH R:3544 , HOH R:3548 , HOH R:3573 , HOH R:3593 , HOH R:3599 , HOH R:3607 , HOH R:3653 , HOH R:3666 , HOH R:3672
BINDING SITE FOR RESIDUE NAD R 336
06
AC6
SOFTWARE
ASN A:6 , GLY A:7 , GLY A:9 , ARG A:10 , ILE A:11 , ASP A:31 , LEU A:32 , LYS A:75 , SER A:93 , THR A:94 , GLY A:95 , PHE A:97 , THR A:117 , ALA A:118 , CSD A:149 , ASN A:180 , ASN A:311 , TYR A:315 , HOH A:339 , HOH A:345 , HOH A:352 , HOH A:365 , HOH A:404 , HOH A:429 , HOH A:465 , HOH A:466 , HOH A:487 , HOH A:501 , HOH A:507 , LEU D:187 , HOH D:3519
BINDING SITE FOR RESIDUE NAD A 336
07
AC7
SOFTWARE
ASN B:6 , GLY B:7 , GLY B:9 , ARG B:10 , ILE B:11 , ASP B:31 , LEU B:32 , LYS B:75 , SER B:93 , THR B:94 , GLY B:95 , PHE B:97 , THR B:117 , ALA B:118 , CSD B:149 , ASN B:180 , ASN B:311 , TYR B:315 , HOH B:340 , HOH B:341 , HOH B:356 , HOH B:366 , HOH B:370 , HOH B:377 , HOH B:395 , HOH B:409 , HOH B:410 , HOH B:415 , HOH B:449 , HOH B:474 , LEU C:187 , HOH C:1824
BINDING SITE FOR RESIDUE NAD B 336
08
AC8
SOFTWARE
LEU B:187 , HOH B:338 , ASN C:6 , GLY C:7 , GLY C:9 , ARG C:10 , ILE C:11 , ASN C:30 , ASP C:31 , LEU C:32 , LYS C:75 , SER C:93 , THR C:94 , GLY C:95 , PHE C:97 , THR C:117 , ALA C:118 , CSD C:149 , ASN C:180 , ASN C:311 , TYR C:315 , HOH C:1802 , HOH C:1803 , HOH C:1815 , HOH C:1833 , HOH C:1847 , HOH C:1895 , HOH C:1917 , HOH C:1918 , HOH C:1945 , HOH C:1961 , HOH C:1994
BINDING SITE FOR RESIDUE NAD C 336
09
AC9
SOFTWARE
LEU A:187 , HOH A:346 , ASN D:6 , GLY D:7 , GLY D:9 , ARG D:10 , ILE D:11 , ASP D:31 , LEU D:32 , LYS D:75 , SER D:93 , THR D:94 , GLY D:95 , PHE D:97 , THR D:117 , ALA D:118 , CSD D:149 , ASN D:180 , ASN D:311 , TYR D:315 , HOH D:3509 , HOH D:3517 , HOH D:3530 , HOH D:3536 , HOH D:3547 , HOH D:3564 , HOH D:3579 , HOH D:3590 , HOH D:3595 , HOH D:3650
BINDING SITE FOR RESIDUE NAD D 336
10
BC1
SOFTWARE
ASP C:65 , NA C:1600 , HOH C:1853 , HOH C:1996 , HOH C:1998 , ASP Q:65 , HOH Q:3563 , HOH Q:3699 , HOH Q:3722
BINDING SITE FOR RESIDUE PGE C 1700
11
BC2
SOFTWARE
HOH C:1862 , HOH Q:3736 , GLY R:222
BINDING SITE FOR RESIDUE IPA C 1800
12
BC3
SOFTWARE
GLY D:222 , GLU Q:248 , HOH Q:3546 , HOH Q:3736
BINDING SITE FOR RESIDUE IPA Q 1801
13
BC4
SOFTWARE
GLU Q:276 , LYS Q:294 , LEU Q:295 , ARG R:193 , THR R:206 , HOH R:3623
BINDING SITE FOR RESIDUE GOL R 3502
14
BC5
SOFTWARE
ARG Q:193 , THR Q:206 , GLU R:276 , LYS R:294
BINDING SITE FOR RESIDUE GOL Q 3503
15
BC6
SOFTWARE
GLU C:276 , LEU C:295 , ARG D:193 , THR D:205 , THR D:206 , MET D:227 , HOH D:3637
BINDING SITE FOR RESIDUE GOL D 3504
[
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
(1, 8)
Info
All PROSITE Patterns/Profiles
1: GAPDH (A:147-154,B:147-154,C:147-154,D:14...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
GAPDH
PS00071
Glyceraldehyde 3-phosphate dehydrogenase active site.
G3P_THEAQ
147-154
8
A:147-154
B:147-154
C:147-154
D:147-154
O:147-154
P:147-154
Q:147-154
R:147-154
[
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
(2, 16)
Info
All SCOP Domains
1a: SCOP_d2g82a2 (A:149-310)
1b: SCOP_d2g82b2 (B:149-310)
1c: SCOP_d2g82c2 (C:149-310)
1d: SCOP_d2g82d2 (D:149-310)
1e: SCOP_d2g82o2 (O:149-310)
1f: SCOP_d2g82p2 (P:149-310)
1g: SCOP_d2g82q2 (Q:149-310)
1h: SCOP_d2g82r2 (R:149-310)
2a: SCOP_d2g82a1 (A:1-148,A:311-330)
2b: SCOP_d2g82b1 (B:1-148,B:311-330)
2c: SCOP_d2g82c1 (C:1-148,C:311-330)
2d: SCOP_d2g82d1 (D:1-148,D:311-330)
2e: SCOP_d2g82o1 (O:1-148,O:311-330)
2f: SCOP_d2g82p1 (P:1-148,P:311-330)
2g: SCOP_d2g82q1 (Q:1-148,Q:311-330)
2h: SCOP_d2g82r1 (R:1-148,R:311-330)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
FwdE/GAPDH domain-like
(188)
Superfamily
:
Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
(179)
Family
:
GAPDH-like
(99)
Protein domain
:
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)
(61)
Thermus aquaticus [TaxId: 271]
(2)
1a
d2g82a2
A:149-310
1b
d2g82b2
B:149-310
1c
d2g82c2
C:149-310
1d
d2g82d2
D:149-310
1e
d2g82o2
O:149-310
1f
d2g82p2
P:149-310
1g
d2g82q2
Q:149-310
1h
d2g82r2
R:149-310
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
:
Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
(179)
Protein domain
:
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)
(61)
Thermus aquaticus [TaxId: 271]
(2)
2a
d2g82a1
A:1-148,A:311-330
2b
d2g82b1
B:1-148,B:311-330
2c
d2g82c1
C:1-148,C:311-330
2d
d2g82d1
D:1-148,D:311-330
2e
d2g82o1
O:1-148,O:311-330
2f
d2g82p1
P:1-148,P:311-330
2g
d2g82q1
Q:1-148,Q:311-330
2h
d2g82r1
R:1-148,R:311-330
[
close SCOP info
]
CATH Domains
(2, 16)
Info
all CATH domains
1a: CATH_2g82A02 (A:148-311)
1b: CATH_2g82B02 (B:148-311)
1c: CATH_2g82C02 (C:148-311)
1d: CATH_2g82D02 (D:148-311)
1e: CATH_2g82O02 (O:148-311)
1f: CATH_2g82P02 (P:148-311)
1g: CATH_2g82Q02 (Q:148-311)
1h: CATH_2g82R02 (R:148-311)
2a: CATH_2g82A01 (A:1-147,A:312-330)
2b: CATH_2g82B01 (B:1-147,B:312-330)
2c: CATH_2g82C01 (C:1-147,C:312-330)
2d: CATH_2g82D01 (D:1-147,D:312-330)
2e: CATH_2g82O01 (O:1-147,O:312-330)
2f: CATH_2g82P01 (P:1-147,P:312-330)
2g: CATH_2g82Q01 (Q:1-147,Q:312-330)
2h: CATH_2g82R01 (R:1-147,R:312-330)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Dihydrodipicolinate Reductase; domain 2
(182)
Homologous Superfamily
:
Dihydrodipicolinate Reductase; domain 2
(178)
Thermus aquaticus. Organism_taxid: 271.
(2)
1a
2g82A02
A:148-311
1b
2g82B02
B:148-311
1c
2g82C02
C:148-311
1d
2g82D02
D:148-311
1e
2g82O02
O:148-311
1f
2g82P02
P:148-311
1g
2g82Q02
Q:148-311
1h
2g82R02
R:148-311
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Thermus aquaticus. Organism_taxid: 271.
(3)
2a
2g82A01
A:1-147,A:312-330
2b
2g82B01
B:1-147,B:312-330
2c
2g82C01
C:1-147,C:312-330
2d
2g82D01
D:1-147,D:312-330
2e
2g82O01
O:1-147,O:312-330
2f
2g82P01
P:1-147,P:312-330
2g
2g82Q01
Q:1-147,Q:312-330
2h
2g82R01
R:1-147,R:312-330
[
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
Chain O
Chain P
Chain Q
Chain R
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 (450 KB)
Header - Asym.Unit
Biol.Unit 1 (226 KB)
Header - Biol.Unit 1
Biol.Unit 2 (221 KB)
Header - Biol.Unit 2
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
2G82
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
