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.
4GKX
Asym. Unit
Info
Asym.Unit (247 KB)
Biol.Unit 1 (45 KB)
Biol.Unit 2 (44 KB)
Biol.Unit 3 (44 KB)
Biol.Unit 4 (44 KB)
Biol.Unit 5 (44 KB)
Biol.Unit 6 (44 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF A CARBOHYDRATE-BINDING DOMAIN
Authors
:
R. C. Page, C. Zheng, J. C. Nix, S. Misra, B. Zhang
Date
:
13 Aug 12 (Deposition) - 05 Jun 13 (Release) - 31 Jul 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Biol. Unit 5: E (1x)
Biol. Unit 6: F (1x)
Keywords
:
Protein Transport, Endoplasmic Reticulum
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Zheng, R. C. Page, V. Das, J. C. Nix, E. Wigren, S. Misra, B. Zhang
Structural Characterization Of Carbohydrate Binding By Lman Protein Provides New Insight Into The Endoplasmic Reticulum Export Of Factors V (Fv) And Viii (Fviii).
J. Biol. Chem. V. 288 20499 2013
[
close entry info
]
Hetero Components
(3, 25)
Info
All Hetero Components
1a: 2-O-ALPHA-D-MANNOPYRANOSYL-ALPHA-D... (2M4a)
1b: 2-O-ALPHA-D-MANNOPYRANOSYL-ALPHA-D... (2M4b)
1c: 2-O-ALPHA-D-MANNOPYRANOSYL-ALPHA-D... (2M4c)
1d: 2-O-ALPHA-D-MANNOPYRANOSYL-ALPHA-D... (2M4d)
1e: 2-O-ALPHA-D-MANNOPYRANOSYL-ALPHA-D... (2M4e)
1f: 2-O-ALPHA-D-MANNOPYRANOSYL-ALPHA-D... (2M4f)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
2e: CALCIUM ION (CAe)
2f: CALCIUM ION (CAf)
2g: CALCIUM ION (CAg)
2h: CALCIUM ION (CAh)
2i: CALCIUM ION (CAi)
2j: CALCIUM ION (CAj)
2k: CALCIUM ION (CAk)
2l: CALCIUM ION (CAl)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
3f: GLYCEROL (GOLf)
3g: GLYCEROL (GOLg)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
2M4
6
Ligand/Ion
2-O-ALPHA-D-MANNOPYRANOSYL-ALPHA-D-MANNOPYRANOSE
2
CA
12
Ligand/Ion
CALCIUM ION
3
GOL
7
Ligand/Ion
GLYCEROL
[
close Hetero Component info
]
Sites
(25, 25)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:152 , PHE A:154 , ASN A:156 , ASP A:181 , HOH A:448
BINDING SITE FOR RESIDUE CA A 301
02
AC2
SOFTWARE
ASP A:155 , ASP A:157 , ASN A:161 , ASN A:162 , ASP A:181 , HOH A:446
BINDING SITE FOR RESIDUE CA A 302
03
AC3
SOFTWARE
ASP A:121 , PHE A:154 , ASN A:156 , HIS A:178 , GLY A:251 , GLY A:252 , LEU A:253 , HOH A:457 , HOH A:458
BINDING SITE FOR RESIDUE 2M4 A 303
04
AC4
SOFTWARE
ARG A:45 , GLU B:102
BINDING SITE FOR RESIDUE GOL A 304
05
AC5
SOFTWARE
PHE A:229 , ALA A:231 , LYS A:232
BINDING SITE FOR RESIDUE GOL A 305
06
AC6
SOFTWARE
ASN A:130 , LEU A:143 , TRP A:144 , ASN A:145
BINDING SITE FOR RESIDUE GOL A 306
07
AC7
SOFTWARE
LYS A:49 , PHE A:66 , THR A:97 , PHE A:220 , THR A:221 , ASP A:226 , HOH A:418 , HOH A:420
BINDING SITE FOR RESIDUE GOL A 307
08
AC8
SOFTWARE
HOH A:456
BINDING SITE FOR RESIDUE GOL A 308
09
AC9
SOFTWARE
ASP B:152 , PHE B:154 , ASN B:156 , ASP B:181 , HOH B:435
BINDING SITE FOR RESIDUE CA B 301
10
BC1
SOFTWARE
ASP B:155 , ASP B:157 , ASN B:161 , ASN B:162 , ASP B:181
BINDING SITE FOR RESIDUE CA B 302
11
BC2
SOFTWARE
ALA B:120 , ASP B:121 , PHE B:154 , ASN B:156 , HIS B:178 , GLY B:251 , GLY B:252 , LEU B:253 , HOH B:434 , HOH B:459 , HOH B:460 , HOH B:461
BINDING SITE FOR RESIDUE 2M4 B 303
12
BC3
SOFTWARE
GLY B:71 , HOH B:445
BINDING SITE FOR RESIDUE GOL B 304
13
BC4
SOFTWARE
ASP C:152 , PHE C:154 , ASN C:156 , ASP C:181 , HOH C:435
BINDING SITE FOR RESIDUE CA C 301
14
BC5
SOFTWARE
ASP C:155 , ASP C:157 , ASN C:161 , ASN C:162 , ASP C:181
BINDING SITE FOR RESIDUE CA C 302
15
BC6
SOFTWARE
ALA C:120 , ASP C:121 , PHE C:154 , ASN C:156 , HIS C:178 , GLY C:251 , GLY C:252 , LEU C:253 , HOH C:463
BINDING SITE FOR RESIDUE 2M4 C 303
16
BC7
SOFTWARE
HOH C:437 , HOH C:456
BINDING SITE FOR RESIDUE GOL C 304
17
BC8
SOFTWARE
ASP D:152 , PHE D:154 , ASN D:156 , ASP D:181 , HOH D:446
BINDING SITE FOR RESIDUE CA D 301
18
BC9
SOFTWARE
ASP D:155 , ASP D:157 , ASN D:161 , ASN D:162 , ASP D:181
BINDING SITE FOR RESIDUE CA D 302
19
CC1
SOFTWARE
ALA D:120 , ASP D:121 , ASN D:156 , HIS D:178 , GLY D:251 , GLY D:252 , LEU D:253 , HOH D:454 , HOH D:455 , HOH D:456
BINDING SITE FOR RESIDUE 2M4 D 303
20
CC2
SOFTWARE
ASP E:152 , PHE E:154 , ASN E:156 , ASP E:181 , HOH E:423
BINDING SITE FOR RESIDUE CA E 301
21
CC3
SOFTWARE
ASP E:155 , ASP E:157 , ASN E:161 , ASN E:162 , ASP E:181
BINDING SITE FOR RESIDUE CA E 302
22
CC4
SOFTWARE
ALA E:120 , ASP E:121 , PHE E:154 , ASN E:156 , HIS E:178 , GLY E:251 , GLY E:252 , LEU E:253 , HOH E:442
BINDING SITE FOR RESIDUE 2M4 E 303
23
CC5
SOFTWARE
ASP F:152 , PHE F:154 , ASN F:156 , ASP F:181 , HOH F:436
BINDING SITE FOR RESIDUE CA F 301
24
CC6
SOFTWARE
ASP F:155 , ASP F:157 , ASN F:161 , ASN F:162 , ASP F:181
BINDING SITE FOR RESIDUE CA F 302
25
CC7
SOFTWARE
ALA F:120 , ASP F:121 , PHE F:154 , ASN F:156 , HIS F:178 , GLY F:251 , GLY F:252 , LEU F:253
BINDING SITE FOR RESIDUE 2M4 F 303
[
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, 6)
Info
All SCOP Domains
1a: SCOP_d4gkxa_ (A:)
1b: SCOP_d4gkxf_ (F:)
1c: SCOP_d4gkxb_ (B:)
1d: SCOP_d4gkxc_ (C:)
1e: SCOP_d4gkxd_ (D:)
1f: SCOP_d4gkxe_ (E:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Concanavalin A-like lectins/glucanases
(797)
Superfamily
:
Concanavalin A-like lectins/glucanases
(797)
Family
:
Lectin leg-like
(18)
Protein domain
:
automated matches
(10)
Human (Homo sapiens) [TaxId: 9606]
(7)
1a
d4gkxa_
A:
1b
d4gkxf_
F:
1c
d4gkxb_
B:
1d
d4gkxc_
C:
1e
d4gkxd_
D:
1f
d4gkxe_
E:
[
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
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 (247 KB)
Header - Asym.Unit
Biol.Unit 1 (45 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
Biol.Unit 5 (44 KB)
Header - Biol.Unit 5
Biol.Unit 6 (44 KB)
Header - Biol.Unit 6
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
4GKX
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help