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.
1K55
Biol. Unit 2
Info
Asym.Unit (367 KB)
Biol.Unit 1 (178 KB)
Biol.Unit 2 (187 KB)
Biol.Unit 3 (360 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
OXA 10 CLASS D BETA-LACTAMASE AT PH 7.5
Authors
:
D. Golemi, L. Maveyraud, S. Vakulenko, J. P. Samama, S. Mobashery
Date
:
10 Oct 01 (Deposition) - 07 Nov 01 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.39
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,C (1x)
Biol. Unit 2: B,D (1x)
Biol. Unit 3: A,B,C,D (1x)
Keywords
:
Beta-Lactamase, Antibiotic Resistance, Carbamylation, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Golemi, L. Maveyraud, S. Vakulenko, J. P. Samama, S. Mobashery
Critical Involvement Of A Carbamylated Lysine In Catalytic Function Of Class D Beta-Lactamases.
Proc. Natl. Acad. Sci. Usa V. 98 14280 2001
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 18)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
1d: 1,2-ETHANEDIOL (EDOd)
1e: 1,2-ETHANEDIOL (EDOe)
1f: 1,2-ETHANEDIOL (EDOf)
1g: 1,2-ETHANEDIOL (EDOg)
1h: 1,2-ETHANEDIOL (EDOh)
1i: 1,2-ETHANEDIOL (EDOi)
2a: LYSINE NZ-CARBOXYLIC ACID (KCXa)
2b: LYSINE NZ-CARBOXYLIC ACID (KCXb)
2c: LYSINE NZ-CARBOXYLIC ACID (KCXc)
2d: LYSINE NZ-CARBOXYLIC ACID (KCXd)
3a: SULFATE ION (SO4a)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
6
Ligand/Ion
1,2-ETHANEDIOL
2
KCX
2
Mod. Amino Acid
LYSINE NZ-CARBOXYLIC ACID
3
SO4
10
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(18, 18)
Info
All Sites
01: BC1 (SOFTWARE)
02: BC2 (SOFTWARE)
03: BC3 (SOFTWARE)
04: BC4 (SOFTWARE)
05: BC5 (SOFTWARE)
06: BC6 (SOFTWARE)
07: BC7 (SOFTWARE)
08: BC8 (SOFTWARE)
09: BC9 (SOFTWARE)
10: CC1 (SOFTWARE)
11: CC2 (SOFTWARE)
12: CC3 (SOFTWARE)
13: CC4 (SOFTWARE)
14: CC5 (SOFTWARE)
15: CC6 (SOFTWARE)
16: CC7 (SOFTWARE)
17: CC8 (SOFTWARE)
18: CC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
BC1
SOFTWARE
SER B:67 , SER B:115 , LYS B:205 , THR B:206 , GLY B:207 , PHE B:208 , ARG B:250 , SO4 B:1011 , HOH B:1044 , HOH B:1147 , HOH B:1257
BINDING SITE FOR RESIDUE SO4 B 1001
02
BC2
SOFTWARE
THR B:206 , ARG B:250 , SO4 B:1001 , HOH B:1147 , HOH B:1271
BINDING SITE FOR RESIDUE SO4 B 1011
03
BC3
SOFTWARE
ARG B:131 , LYS B:134 , TYR B:135 , HOH B:1215
BINDING SITE FOR RESIDUE SO4 B 1021
04
BC4
SOFTWARE
ARG B:160 , HOH B:1308
BINDING SITE FOR RESIDUE SO4 B 1022
05
BC5
SOFTWARE
MET B:99 , LYS B:100 , GLN B:101 , HOH B:1216 , HOH B:1221
BINDING SITE FOR RESIDUE SO4 B 1023
06
BC6
SOFTWARE
ASN B:29 , PHE B:32 , VAL B:37 , ASN B:38 , GLY B:39 , ASN B:54 , HOH B:1180
BINDING SITE FOR RESIDUE EDO B 1033
07
BC7
SOFTWARE
PRO B:217 , ASP B:240 , ASP B:242 , HOH B:1050 , HOH B:1072 , HOH B:1164 , HOH B:1199
BINDING SITE FOR RESIDUE EDO B 1037
08
BC8
SOFTWARE
LYS B:95 , SER C:115 , LYS C:205 , THR C:206 , GLY C:207 , PHE C:208 , ARG C:250 , HOH C:1053
BINDING SITE FOR RESIDUE SO4 C 1005
09
BC9
SOFTWARE
LYS B:152 , THR C:213 , HOH C:1118
BINDING SITE FOR RESIDUE SO4 C 1019
10
CC1
SOFTWARE
LYS A:95 , SER D:67 , SER D:115 , THR D:206 , GLY D:207 , PHE D:208 , ARG D:250 , SO4 D:1024 , HOH D:1081
BINDING SITE FOR RESIDUE SO4 D 1003
11
CC2
SOFTWARE
HOH B:1245 , SER D:181 , LYS D:182
BINDING SITE FOR RESIDUE SO4 D 1009
12
CC3
SOFTWARE
ARG D:250 , LYS D:251 , HOH D:1291 , HOH D:1301 , HOH D:1308
BINDING SITE FOR RESIDUE SO4 D 1014
13
CC4
SOFTWARE
HOH A:1206 , LYS D:152 , HOH D:1203 , HOH D:1241
BINDING SITE FOR RESIDUE SO4 D 1020
14
CC5
SOFTWARE
SER D:67 , LYS D:70 , TRP D:102 , VAL D:114 , SER D:115 , ALA D:116 , VAL D:117 , SO4 D:1003 , HOH D:1273
BINDING SITE FOR RESIDUE SO4 D 1024
15
CC6
SOFTWARE
ARG B:109 , ALA D:197 , PRO D:198 , GLU D:199 , TYR D:200 , GLU D:229 , HOH D:1044
BINDING SITE FOR RESIDUE EDO D 1034
16
CC7
SOFTWARE
TYR D:200 , THR D:255 , MET D:258 , ILE D:264 , EDO D:1036
BINDING SITE FOR RESIDUE EDO D 1035
17
CC8
SOFTWARE
ILE D:264 , EDO D:1035 , HOH D:1311
BINDING SITE FOR RESIDUE EDO D 1036
18
CC9
SOFTWARE
LYS A:91 , HOH A:1113 , MET D:99 , LYS D:100 , GLN D:101
BINDING SITE FOR RESIDUE EDO D 1040
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: BETA_LACTAMASE_D (B:65-75,D:65-75)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
BETA_LACTAMASE_D
PS00337
Beta-lactamase class-D active site.
BLO10_PSEAI
65-75
2
-
B:65-75
-
D:65-75
[
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_d1k55a_ (A:)
1b: SCOP_d1k55b_ (B:)
1c: SCOP_d1k55c_ (C:)
1d: SCOP_d1k55d_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
beta-lactamase/transpeptidase-like
(515)
Superfamily
:
beta-lactamase/transpeptidase-like
(515)
Family
:
beta-Lactamase/D-ala carboxypeptidase
(411)
Protein domain
:
Class D beta-lactamase
(32)
Pseudomonas aeruginosa, OXA-10 [TaxId: 287]
(25)
1a
d1k55a_
A:
1b
d1k55b_
B:
1c
d1k55c_
C:
1d
d1k55d_
D:
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1k55C00 (C:21-266)
1b: CATH_1k55A00 (A:21-265)
1c: CATH_1k55B00 (B:21-265)
1d: CATH_1k55D00 (D:21-266)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Beta-lactamase
(339)
Homologous Superfamily
:
DD-peptidase/beta-lactamase superfamily
(335)
Pseudomonas aeruginosa. Organism_taxid: 287.
(17)
1a
1k55C00
C:21-266
1b
1k55A00
A:21-265
1c
1k55B00
B:21-265
1d
1k55D00
D:21-266
[
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 B
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 (367 KB)
Header - Asym.Unit
Biol.Unit 1 (178 KB)
Header - Biol.Unit 1
Biol.Unit 2 (187 KB)
Header - Biol.Unit 2
Biol.Unit 3 (360 KB)
Header - Biol.Unit 3
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
1K55
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help