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.
4BF5
Asym. Unit
Info
Asym.Unit (268 KB)
Biol.Unit 1 (261 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF BROAD SPECTRUM RACEMASE FROM AEROMONAS HYDROPHILA
Authors
:
C. Carrasco-Lopez, J. A. Hermoso
Date
:
15 Mar 13 (Deposition) - 15 Jan 14 (Release) - 09 Jul 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.45
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Isomerase, D-Amino Acids
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Espaillat, C. Carrasco-Lopez, N. Bernardo-Garcia, N. Pietrosemoli, L. H. Otero, L. Alvarez, M. A. De Pedro, F. Pazos, B. M. Davis, M. K. Waldor, J. A. Hermoso, F. Cava
Structural Basis For The Broad Specificity Of A New Family Of Amino-Acid Racemases.
Acta Crystallogr. , Sect. D V. 70 79 2014
[
close entry info
]
Hetero Components
(4, 33)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
1e: CHLORIDE ION (CLe)
1f: CHLORIDE ION (CLf)
1g: CHLORIDE ION (CLg)
1h: CHLORIDE ION (CLh)
1i: CHLORIDE ION (CLi)
1j: CHLORIDE ION (CLj)
1k: CHLORIDE ION (CLk)
1l: CHLORIDE ION (CLl)
1m: CHLORIDE ION (CLm)
1n: CHLORIDE ION (CLn)
1o: CHLORIDE ION (CLo)
1p: CHLORIDE ION (CLp)
1q: CHLORIDE ION (CLq)
1r: CHLORIDE ION (CLr)
1s: CHLORIDE ION (CLs)
1t: CHLORIDE ION (CLt)
1u: CHLORIDE ION (CLu)
1v: CHLORIDE ION (CLv)
1w: CHLORIDE ION (CLw)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
3a: NICKEL (II) ION (NIa)
4a: PYRIDOXAL-5'-PHOSPHATE (PLPa)
4b: PYRIDOXAL-5'-PHOSPHATE (PLPb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
23
Ligand/Ion
CHLORIDE ION
2
GOL
7
Ligand/Ion
GLYCEROL
3
NI
1
Ligand/Ion
NICKEL (II) ION
4
PLP
2
Ligand/Ion
PYRIDOXAL-5'-PHOSPHATE
[
close Hetero Component info
]
Sites
(28, 28)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LYS A:74 , TYR A:78 , HIS A:204 , SER A:245 , ARG A:260 , GLY A:262 , GLY A:263 , HOH A:2173 , HOH A:2291 , HOH A:2301
BINDING SITE FOR RESIDUE PLP A1350
02
AC2
SOFTWARE
HIS A:417 , HOH A:2403 , HOH A:2404 , LYS B:74 , TYR B:78 , VAL B:120 , ARG B:173 , HIS B:204 , SER B:245 , ARG B:260 , GLY B:262 , GLY B:263 , HOH B:2168 , HOH B:2255 , HOH B:2385
BINDING SITE FOR RESIDUE PLP B1350
03
AC3
SOFTWARE
TYR A:24 , HOH A:2002 , ASN B:33 , GLY B:399 , TYR B:400 , ASN B:402 , LYS B:404 , HOH B:2108 , HOH B:2109 , HOH B:2426
BINDING SITE FOR RESIDUE GOL B1418
04
AC4
SOFTWARE
ALA A:39 , SER A:40 , ASN A:41 , PRO A:403 , HOH A:2051 , ALA B:22 , SER B:101 , ASN B:102 , GLU B:103 , GLU B:127
BINDING SITE FOR RESIDUE GOL B1419
05
AC5
SOFTWARE
ARG A:173 , ASN A:174 , HIS A:204
BINDING SITE FOR RESIDUE CL A1418
06
AC6
SOFTWARE
ARG B:173 , ASN B:174 , HIS B:204
BINDING SITE FOR RESIDUE CL B1420
07
AC7
SOFTWARE
ARG A:324
BINDING SITE FOR RESIDUE CL A1419
08
AC8
SOFTWARE
HOH A:2080
BINDING SITE FOR RESIDUE CL A1421
09
AC9
SOFTWARE
ASP A:253
BINDING SITE FOR RESIDUE CL A1422
10
BC1
SOFTWARE
ARG A:109
BINDING SITE FOR RESIDUE CL A1423
11
BC2
SOFTWARE
GLY A:337 , HOH A:2214 , HOH A:2218
BINDING SITE FOR RESIDUE CL A1424
12
BC3
SOFTWARE
ASP B:253
BINDING SITE FOR RESIDUE CL B1421
13
BC4
SOFTWARE
LYS B:210 , HOH B:2299
BINDING SITE FOR RESIDUE CL B1422
14
BC5
SOFTWARE
GLY A:49 , ARG A:408 , SER B:272
BINDING SITE FOR RESIDUE CL B1423
15
BC6
SOFTWARE
HIS B:414 , HIS B:416 , NI B:1430
BINDING SITE FOR RESIDUE CL B1424
16
BC7
SOFTWARE
GLU A:129 , GLN A:130
BINDING SITE FOR RESIDUE CL A1425
17
BC8
SOFTWARE
ILE B:69 , HOH B:2076 , HOH B:2096
BINDING SITE FOR RESIDUE CL B1426
18
BC9
SOFTWARE
HOH B:2004
BINDING SITE FOR RESIDUE CL A1426
19
CC1
SOFTWARE
HOH B:2146
BINDING SITE FOR RESIDUE CL B1427
20
CC2
SOFTWARE
ARG B:324 , TRP B:398 , GOL B:1432 , HOH B:2427
BINDING SITE FOR RESIDUE CL B1428
21
CC3
SOFTWARE
HOH B:2195
BINDING SITE FOR RESIDUE CL B1429
22
CC4
SOFTWARE
HIS B:414 , HIS B:416 , CL B:1424
BINDING SITE FOR RESIDUE NI B1430
23
CC5
SOFTWARE
ALA A:22 , SER A:101 , ASN A:102 , GLU A:103 , GLU A:127 , HOH A:2499 , ALA B:39 , SER B:40 , ASN B:41 , PRO B:403
BINDING SITE FOR RESIDUE GOL A1428
24
CC6
SOFTWARE
VAL A:289 , TRP A:311 , VAL A:355 , LEU A:358 , LYS A:359 , GLY A:360 , VAL A:361 , HOH A:2500
BINDING SITE FOR RESIDUE GOL A1430
25
CC7
SOFTWARE
TYR A:332 , LYS A:339 , ALA A:376 , GLU A:377 , HOH A:2501
BINDING SITE FOR RESIDUE GOL A1431
26
CC8
SOFTWARE
ARG B:116
BINDING SITE FOR RESIDUE CL B1431
27
CC9
SOFTWARE
ARG B:324 , ARG B:325 , ALA B:326 , ASN B:329 , MET B:394 , CL B:1428 , HOH B:2408
BINDING SITE FOR RESIDUE GOL B1432
28
DC1
SOFTWARE
LYS B:359 , GLY B:360 , HOH B:2428
BINDING SITE FOR RESIDUE GOL B1433
[
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
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
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
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 (268 KB)
Header - Asym.Unit
Biol.Unit 1 (261 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
4BF5
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
