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.
1QIP
Biol. Unit 1
Info
Asym.Unit (144 KB)
Biol.Unit 1 (71 KB)
Biol.Unit 2 (71 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
HUMAN GLYOXALASE I COMPLEXED WITH S-P-NITROBENZYLOXYCARBONYLGLUTATHIONE
Authors
:
A. D. Cameron, M. Ridderstrom, B. Olin, B. Mannervik
Date
:
14 Jun 99 (Deposition) - 24 Nov 99 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.72
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Lyase, Lactoylglutathione Lyase, Glyoxalase I
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. D. Cameron, M. Ridderstrom, B. Olin, M. J. Kavarana, D. J. Creighton B. Mannervik
Reaction Mechanism Of Glyoxalase I Explored By An X-Ray Crystallographic Analysis Of The Human Enzyme In Complex With A Transition State Analogue.
Biochemistry V. 38 13480 1999
[
close entry info
]
Hetero Components
(2, 4)
Info
All Hetero Components
1a: BETA-MERCAPTOETHANOL (BMEa)
1b: BETA-MERCAPTOETHANOL (BMEb)
1c: BETA-MERCAPTOETHANOL (BMEc)
1d: BETA-MERCAPTOETHANOL (BMEd)
2a: S-P-NITROBENZYLOXYCARBONYLGLUTATHI... (GNBa)
2b: S-P-NITROBENZYLOXYCARBONYLGLUTATHI... (GNBb)
2c: S-P-NITROBENZYLOXYCARBONYLGLUTATHI... (GNBc)
2d: S-P-NITROBENZYLOXYCARBONYLGLUTATHI... (GNBd)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
3c: ZINC ION (ZNc)
3d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BME
2
Ligand/Ion
BETA-MERCAPTOETHANOL
2
GNB
2
Ligand/Ion
S-P-NITROBENZYLOXYCARBONYLGLUTATHIONE
3
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(13, 13)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC5 (SOFTWARE)
04: AC6 (SOFTWARE)
05: AC7 (SOFTWARE)
06: AC9 (SOFTWARE)
07: BC1 (SOFTWARE)
08: GH1 (AUTHOR)
09: GH2 (AUTHOR)
10: HD2 (AUTHOR)
11: HD3 (AUTHOR)
12: ZN1 (AUTHOR)
13: ZN2 (AUTHOR)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:126 , GLU A:172 , HOH A:1227 , HOH A:1228 , GLN B:33 , GLU B:99
BINDING SITE FOR RESIDUE ZN B 901
02
AC2
SOFTWARE
GLN A:33 , GLU A:99 , HOH A:1229 , HIS B:126 , GLU B:172 , HOH B:1225
BINDING SITE FOR RESIDUE ZN A 902
03
AC5
SOFTWARE
ARG A:122 , LEU A:160 , PHE A:162 , GLU A:172 , MET A:179 , LEU A:182 , HOH A:1227 , ARG B:37 , CYS B:60 , PHE B:67 , ILE B:88 , LEU B:92 , THR B:101 , ASN B:103 , BME B:204 , HOH B:1006 , HOH B:1040 , HOH B:1100 , HOH B:1102 , HOH B:1107 , HOH B:1113 , HOH B:1125 , HOH B:1129 , HOH B:1197 , SER C:17
BINDING SITE FOR RESIDUE GNB B 1001
04
AC6
SOFTWARE
ARG A:37 , GLN A:58 , CYS A:60 , PHE A:67 , PHE A:71 , ILE A:88 , LEU A:92 , THR A:101 , ASN A:103 , BME A:204 , HOH A:1037 , HOH A:1112 , HOH A:1138 , HOH A:1178 , ARG B:122 , MET B:157 , LEU B:160 , PHE B:162 , TRP B:170 , ASP D:154 , LYS D:158 , HOH D:1005
BINDING SITE FOR RESIDUE GNB A 1002
05
AC7
SOFTWARE
SER A:17 , HOH A:1116 , ARG C:122 , MET C:157 , LEU C:160 , PHE C:162 , MET C:179 , HOH C:1061 , ARG D:37 , CYS D:60 , PHE D:67 , ILE D:88 , LEU D:92 , THR D:101 , ASN D:103 , BME D:204 , HOH D:1049 , HOH D:1104 , HOH D:1105 , HOH D:1109 , HOH D:1114 , HOH D:1117 , HOH D:1125 , HOH D:1128 , HOH D:1194
BINDING SITE FOR RESIDUE GNB D 1003
06
AC9
SOFTWARE
GLN A:58 , LYS A:59 , CYS A:60 , PHE A:62 , GNB A:1002
BINDING SITE FOR RESIDUE BME A 204
07
BC1
SOFTWARE
GLN B:58 , LYS B:59 , CYS B:60 , LYS B:84 , GNB B:1001 , HOH B:1222
BINDING SITE FOR RESIDUE BME B 204
08
GH1
AUTHOR
ARG A:37 , ASN A:103 , ARG B:122
BINDING SITE FOR GSH MOIETY - SUBSTRATE BINDING SITE IS FORMED BY ZN2 HYD2 AND GSH2.
09
GH2
AUTHOR
ARG B:37 , ASN B:103 , ARG A:122
BINDING SITE FOR GSH MOIETY - SUBSTRATE BINDING SITE IS FORMED BY ZN1 HYD1 AND GSH1.
10
HD2
AUTHOR
CYS A:60 , PHE A:62 , MET A:65 , PHE A:67 , LEU A:69 , PHE A:71 , ILE A:88 , LEU A:92 , MET B:157 , LEU B:160 , PHE B:162 , LEU B:174 , MET B:179 , MET B:183
HYDROPHOBIC SUBSTRATE BINDING POCKET AT DIMER INTERFACE.
11
HD3
AUTHOR
CYS B:60 , PHE B:62 , MET B:65 , PHE B:67 , LEU B:69 , PHE B:71 , ILE B:88 , LEU B:92 , MET A:157 , LEU A:160 , PHE A:162 , LEU A:174 , MET A:179 , MET A:183
HYDROPHOBIC SUBSTRATE BINDING POCKET AT DIMER INTERFACE.
12
ZN1
AUTHOR
ZN A:902 , GLN A:33 , GLU A:99 , HIS B:126 , GLU B:172
ZINC BINDING SITE AT DIMER INTERFACE.
13
ZN2
AUTHOR
ZN B:901 , GLN B:33 , GLU B:99 , HIS A:126 , GLU A:172
ZINC BINDING SITE AT DIMER INTERFACE.
[
close Site info
]
SAPs(SNPs)/Variants
(2, 4)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_031078 (C18Y, chain A/B, )
2: VAR_013481 (E110A, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_031078
C
19
Y
LGUL_HUMAN
Polymorphism
17855424
A/B
C
18
Y
2
UniProt
VAR_013481
E
111
A
LGUL_HUMAN
Polymorphism
4746
A/B
E
110
A
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 6)
Info
All PROSITE Patterns/Profiles
1: VOC (A:30-176,B:30-176)
2: GLYOXALASE_I_1 (A:33-54,B:33-54)
3: GLYOXALASE_I_2 (A:117-133,B:117-133)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
VOC
PS51819
Vicinal oxygen chelate (VOC) domain profile.
LGUL_HUMAN
31-177
2
A:30-176
B:30-176
-
-
2
GLYOXALASE_I_1
PS00934
Glyoxalase I signature 1.
LGUL_HUMAN
34-55
2
A:33-54
B:33-54
-
-
3
GLYOXALASE_I_2
PS00935
Glyoxalase I signature 2.
LGUL_HUMAN
118-134
2
A:117-133
B:117-133
-
-
[
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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1qipa_ (A:)
1b: SCOP_d1qipb_ (B:)
1c: SCOP_d1qipc_ (C:)
1d: SCOP_d1qipd_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
(136)
Superfamily
:
Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
(136)
Family
:
Glyoxalase I (lactoylglutathione lyase)
(16)
Protein domain
:
Glyoxalase I (lactoylglutathione lyase)
(10)
Human (Homo sapiens) [TaxId: 9606]
(4)
1a
d1qipa_
A:
1b
d1qipb_
B:
1c
d1qipc_
C:
1d
d1qipd_
D:
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1qipA00 (A:8-183)
1b: CATH_1qipC00 (C:8-183)
1c: CATH_1qipB00 (B:1-183)
1d: CATH_1qipD00 (D:1-183)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Roll
(3276)
Topology
:
2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1
(113)
Homologous Superfamily
:
2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1
(106)
Human (Homo sapiens)
(4)
1a
1qipA00
A:8-183
1b
1qipC00
C:8-183
1c
1qipB00
B:1-183
1d
1qipD00
D:1-183
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Glyoxalase_1qipD01 (D:30-173)
1b: PFAM_Glyoxalase_1qipD02 (D:30-173)
1c: PFAM_Glyoxalase_1qipD03 (D:30-173)
1d: PFAM_Glyoxalase_1qipD04 (D:30-173)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Glyoxalase
(58)
Family
:
Glyoxalase
(34)
Homo sapiens (Human)
(2)
1a
Glyoxalase-1qipD01
D:30-173
1b
Glyoxalase-1qipD02
D:30-173
1c
Glyoxalase-1qipD03
D:30-173
1d
Glyoxalase-1qipD04
D:30-173
[
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 (144 KB)
Header - Asym.Unit
Biol.Unit 1 (71 KB)
Header - Biol.Unit 1
Biol.Unit 2 (71 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
1QIP
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
