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.
4GLV
Asym. Unit
Info
Asym.Unit (168 KB)
Biol.Unit 1 (44 KB)
Biol.Unit 2 (44 KB)
Biol.Unit 3 (44 KB)
Biol.Unit 4 (44 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
OBODY AM3L09 BOUND TO HEN EGG-WHITE LYSOZYME
Authors
:
J. D. Steemson
Date
:
15 Aug 12 (Deposition) - 21 Aug 13 (Release) - 12 Feb 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.57
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Biol. Unit 4: G,H (1x)
Keywords
:
Beta Barrel, Ob-Fold, Protein-Protein Complex, Novel Scaffold, Muraminidase, Enzyme Inhibition, Engineered Binding Protein, Hydrolase-De Novo Protein Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. D. Steemson, M. Baake, J. Rakonjac, V. L. Arcus, M. T. Liddament
Tracking Molecular Recognition At The Atomic Level With A New Protein Scaffold Based On The Ob-Fold.
Plos One V. 9 86050 2014
[
close entry info
]
Hetero Components
(4, 27)
Info
All Hetero Components
1a: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEa)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
2h: GLYCEROL (GOLh)
2i: GLYCEROL (GOLi)
2j: GLYCEROL (GOLj)
2k: GLYCEROL (GOLk)
2l: GLYCEROL (GOLl)
2m: GLYCEROL (GOLm)
2n: GLYCEROL (GOLn)
2o: GLYCEROL (GOLo)
2p: GLYCEROL (GOLp)
2q: GLYCEROL (GOLq)
2r: GLYCEROL (GOLr)
2s: GLYCEROL (GOLs)
2t: GLYCEROL (GOLt)
3a: PHOSPHATE ION (PO4a)
3b: PHOSPHATE ION (PO4b)
3c: PHOSPHATE ION (PO4c)
3d: PHOSPHATE ION (PO4d)
3e: PHOSPHATE ION (PO4e)
4a: SULFATE ION (SO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EPE
1
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2
GOL
20
Ligand/Ion
GLYCEROL
3
PO4
5
Ligand/Ion
PHOSPHATE ION
4
SO4
1
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(27, 27)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:4 , ARG A:5 , CYS A:6 , GLU A:7 , ARG G:14
BINDING SITE FOR RESIDUE PO4 A 201
02
AC2
SOFTWARE
ALA A:11 , ARG A:14 , HIS A:15 , ASP A:87 , ILE A:88
BINDING SITE FOR RESIDUE PO4 A 202
03
AC3
SOFTWARE
ASP A:48 , ARG A:61 , HOH A:330 , LYS B:37 , PHE B:64
BINDING SITE FOR RESIDUE GOL A 203
04
AC4
SOFTWARE
HOH B:303 , HOH B:323
BINDING SITE FOR RESIDUE GOL B 201
05
AC5
SOFTWARE
ARG B:44 , HOH B:307 , GLU G:35 , ASN G:44
BINDING SITE FOR RESIDUE GOL B 202
06
AC6
SOFTWARE
ARG C:21 , GLY C:22 , TYR C:23 , HOH C:325 , TRP D:90
BINDING SITE FOR RESIDUE GOL C 201
07
AC7
SOFTWARE
PHE C:34 , ASP F:43
BINDING SITE FOR RESIDUE GOL C 202
08
AC8
SOFTWARE
SER C:36 , ASN C:39 , ASN C:44
BINDING SITE FOR RESIDUE GOL C 203
09
AC9
SOFTWARE
ARG C:21 , ASN C:93 , LYS C:97
BINDING SITE FOR RESIDUE GOL C 204
10
BC1
SOFTWARE
PHE C:3 , ARG C:14 , HIS C:15 , SER C:86 , ASP C:87 , ILE C:88
BINDING SITE FOR RESIDUE GOL C 205
11
BC2
SOFTWARE
ASN C:19 , TYR C:20 , ARG C:21 , GLY C:22 , ARG D:89
BINDING SITE FOR RESIDUE EPE C 206
12
BC3
SOFTWARE
SER D:42 , GLU D:45 , GLY D:46 , GLY D:47 , ASN E:113 , GLU F:55 , ARG F:56
BINDING SITE FOR RESIDUE GOL D 201
13
BC4
SOFTWARE
ALA E:122 , TRP E:123
BINDING SITE FOR RESIDUE GOL E 201
14
BC5
SOFTWARE
TYR E:20 , ARG E:21 , HOH E:338 , PO4 F:201
BINDING SITE FOR RESIDUE GOL E 202
15
BC6
SOFTWARE
ARG E:14 , HIS E:15 , ASP E:87 , ILE E:88 , HOH E:337
BINDING SITE FOR RESIDUE SO4 E 203
16
BC7
SOFTWARE
HIS D:62 , ARG E:21 , GOL E:202 , ARG F:89 , TRP F:90
BINDING SITE FOR RESIDUE PO4 F 201
17
BC8
SOFTWARE
TRP F:26 , GLU F:45 , GLU F:73
BINDING SITE FOR RESIDUE GOL F 202
18
BC9
SOFTWARE
LYS F:58 , PRO F:60 , PHE F:97 , PRO F:98 , SER F:99
BINDING SITE FOR RESIDUE GOL F 203
19
CC1
SOFTWARE
SER F:71 , ARG F:72
BINDING SITE FOR RESIDUE GOL F 204
20
CC2
SOFTWARE
ILE F:103 , LEU F:104 , ASN F:105 , LYS F:106 , ILE H:103
BINDING SITE FOR RESIDUE GOL F 205
21
CC3
SOFTWARE
ASN A:65 , PRO A:79 , THR F:85 , THR F:86 , HOH F:333
BINDING SITE FOR RESIDUE GOL F 206
22
CC4
SOFTWARE
HIS B:62 , ARG G:21 , ARG H:89 , TRP H:90
BINDING SITE FOR RESIDUE PO4 G 201
23
CC5
SOFTWARE
TRP G:123
BINDING SITE FOR RESIDUE GOL G 202
24
CC6
SOFTWARE
ASN C:65 , LYS G:116 , GLY G:117 , THR H:86 , HOH H:333
BINDING SITE FOR RESIDUE PO4 H 201
25
CC7
SOFTWARE
LYS H:5 , TRP H:8 , GLU H:11
BINDING SITE FOR RESIDUE GOL H 202
26
CC8
SOFTWARE
ASP B:61 , THR H:88 , ARG H:89
BINDING SITE FOR RESIDUE GOL H 203
27
CC9
SOFTWARE
ARG A:114 , GLU H:45
BINDING SITE FOR RESIDUE GOL H 204
[
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
(1, 4)
Info
All SCOP Domains
1a: SCOP_d4glva_ (A:)
1b: SCOP_d4glvc_ (C:)
1c: SCOP_d4glve_ (E:)
1d: SCOP_d4glvg_ (G:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Lysozyme-like
(1361)
Superfamily
:
Lysozyme-like
(1361)
Family
:
C-type lysozyme
(738)
Protein domain
:
Lysozyme
(696)
Chicken (Gallus gallus) [TaxId: 9031]
(459)
1a
d4glva_
A:
1b
d4glvc_
C:
1c
d4glve_
E:
1d
d4glvg_
G:
[
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
Chain C
Chain D
Chain E
Chain F
Chain G
Chain H
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 (168 KB)
Header - Asym.Unit
Biol.Unit 1 (44 KB)
Header - Biol.Unit 1
Biol.Unit 2 (44 KB)
Header - Biol.Unit 2
Biol.Unit 3 (44 KB)
Header - Biol.Unit 3
Biol.Unit 4 (44 KB)
Header - Biol.Unit 4
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
4GLV
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help