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Getting 'Biological Unit' information from database.
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Getting 'Hetero Component' information from database.
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Getting 'Exon' information from database.
4NEH
Asym. Unit
Info
Asym.Unit (606 KB)
Biol.Unit 1 (594 KB)
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(1)
Title
:
AN INTERNAL LIGAND-BOUND, METASTABLE STATE OF A LEUKOCYTE INTEGRIN, AXB2
Authors
:
M. Sen, K. Yuki, T. A. Springer
Date
:
29 Oct 13 (Deposition) - 15 Jan 14 (Release) - 15 Jan 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.75
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Rossmann Fold, , Complement Receptor, Ic3B, Icam-1, Fibrinogen, Denaturated Proteins, Heparin, N-Linked Glycosylation, Membrane, Cell Adhesion
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Sen, K. Yuki, T. A. Springer
An Internal Ligand-Bound, Metastable State Of A Leukocyte Integrin, Alpha X Beta 2.
J. Cell Biol. V. 203 629 2013
[
close entry info
]
Hetero Components
(7, 28)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
2e: CALCIUM ION (CAe)
3a: CHLORIDE ION (CLa)
4a: ALPHA-D-MANNOSE (MANa)
4b: ALPHA-D-MANNOSE (MANb)
4c: ALPHA-D-MANNOSE (MANc)
4d: ALPHA-D-MANNOSE (MANd)
5a: MAGNESIUM ION (MGa)
5b: MAGNESIUM ION (MGb)
7a: N-ACETYL-D-GLUCOSAMINE (NAGa)
7b: N-ACETYL-D-GLUCOSAMINE (NAGb)
7c: N-ACETYL-D-GLUCOSAMINE (NAGc)
7d: N-ACETYL-D-GLUCOSAMINE (NAGd)
7e: N-ACETYL-D-GLUCOSAMINE (NAGe)
7f: N-ACETYL-D-GLUCOSAMINE (NAGf)
7g: N-ACETYL-D-GLUCOSAMINE (NAGg)
7h: N-ACETYL-D-GLUCOSAMINE (NAGh)
7i: N-ACETYL-D-GLUCOSAMINE (NAGi)
7j: N-ACETYL-D-GLUCOSAMINE (NAGj)
7k: N-ACETYL-D-GLUCOSAMINE (NAGk)
7l: N-ACETYL-D-GLUCOSAMINE (NAGl)
7m: N-ACETYL-D-GLUCOSAMINE (NAGm)
6a: SODIUM ION (NAa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
2
Ligand/Ion
BETA-D-MANNOSE
2
CA
5
Ligand/Ion
CALCIUM ION
3
CL
1
Ligand/Ion
CHLORIDE ION
4
MAN
4
Ligand/Ion
ALPHA-D-MANNOSE
5
MG
2
Ligand/Ion
MAGNESIUM ION
6
NA
1
Ligand/Ion
SODIUM ION
7
NAG
13
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
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
ASP A:574 , THR A:576 , ASP A:578 , LEU A:580 , ASP A:582 , HOH A:1204
BINDING SITE FOR RESIDUE CA A 1101
02
AC2
SOFTWARE
SER A:140 , SER A:142 , THR A:207 , CL A:1120 , HOH A:1245 , HOH A:1268
BINDING SITE FOR RESIDUE MG A 1102
03
AC3
SOFTWARE
ASP A:511 , ASN A:513 , ASP A:515 , LEU A:517 , ASP A:519 , HOH A:1261
BINDING SITE FOR RESIDUE CA A 1103
04
AC4
SOFTWARE
ASP A:447 , ASP A:449 , ASP A:451 , SER A:453 , ASP A:455 , HOH A:1311
BINDING SITE FOR RESIDUE CA A 1104
05
AC5
SOFTWARE
SER A:929 , HIS A:930 , VAL A:931 , ASN A:1031 , NAG A:1106
BINDING SITE FOR RESIDUE NAG A 1105
06
AC6
SOFTWARE
NAG A:1105
BINDING SITE FOR RESIDUE NAG A 1106
07
AC7
SOFTWARE
ASN A:70 , NAG A:1108
BINDING SITE FOR RESIDUE NAG A 1107
08
AC8
SOFTWARE
NAG A:1107 , BMA A:1109
BINDING SITE FOR RESIDUE NAG A 1108
09
AC9
SOFTWARE
NAG A:1108
BINDING SITE FOR RESIDUE BMA A 1109
10
BC1
SOFTWARE
PHE A:354 , SER A:357 , PHE A:371 , ASN A:373 , MET A:374 , SER A:375 , GLN A:376 , ASN A:378 , NAG A:1111
BINDING SITE FOR RESIDUE NAG A 1110
11
BC2
SOFTWARE
GLU A:329 , GLN A:376 , NAG A:1110 , BMA A:1112 , MAN A:1113
BINDING SITE FOR RESIDUE NAG A 1111
12
BC3
SOFTWARE
GLU A:329 , NAG A:1111 , MAN A:1113 , MAN A:1115
BINDING SITE FOR RESIDUE BMA A 1112
13
BC4
SOFTWARE
NAG A:1111 , BMA A:1112 , MAN A:1114
BINDING SITE FOR RESIDUE MAN A 1113
14
BC5
SOFTWARE
GLN A:376 , MAN A:1113
BINDING SITE FOR RESIDUE MAN A 1114
15
BC6
SOFTWARE
SER A:327 , GLU A:329 , BMA A:1112 , MAN A:1116
BINDING SITE FOR RESIDUE MAN A 1115
16
BC7
SOFTWARE
SER A:325 , MAN A:1115
BINDING SITE FOR RESIDUE MAN A 1116
17
BC8
SOFTWARE
THR A:657 , ASP A:659 , ASN A:716 , PHE A:717 , THR A:718 , TYR A:741 , NAG A:1118
BINDING SITE FOR RESIDUE NAG A 1117
18
BC9
SOFTWARE
NAG A:1117
BINDING SITE FOR RESIDUE NAG A 1118
19
CC1
SOFTWARE
THR A:801 , ASN A:880
BINDING SITE FOR RESIDUE NAG A 1119
20
CC2
SOFTWARE
SER A:140 , SER A:142 , GLY A:205 , THR A:207 , MG A:1102
BINDING SITE FOR RESIDUE CL A 1120
21
CC3
SOFTWARE
PHE A:328 , GLY A:352 , THR A:355 , TRP A:356
BINDING SITE FOR RESIDUE NA A 1121
22
CC4
SOFTWARE
ASP B:151 , ASN B:207 , ASP B:209 , PRO B:211 , GLU B:212
BINDING SITE FOR RESIDUE CA B 701
23
CC5
SOFTWARE
ASP B:120 , GLU B:325 , HOH B:809 , HOH B:812 , HOH B:860 , HOH B:861
BINDING SITE FOR RESIDUE CA B 702
24
CC6
SOFTWARE
GLU A:318 , SER B:114 , SER B:116 , GLU B:212 , HOH B:801 , HOH B:821
BINDING SITE FOR RESIDUE MG B 703
25
CC7
SOFTWARE
ASN B:94 , PHE B:363 , NAG B:705
BINDING SITE FOR RESIDUE NAG B 704
26
CC8
SOFTWARE
PHE B:363 , ARG B:371 , NAG B:704
BINDING SITE FOR RESIDUE NAG B 705
27
CC9
SOFTWARE
ASN B:620 , ALA B:623 , ALA B:624 , NAG B:707
BINDING SITE FOR RESIDUE NAG B 706
28
DC1
SOFTWARE
NAG B:706
BINDING SITE FOR RESIDUE NAG B 707
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
[
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]
Exons
(0, 0)
Info
All Exons
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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:
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Label:
Sorry, no Info available
[
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
[
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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
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Molecule Coloring
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by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
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by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
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Stereo
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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)
[
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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") .
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Asym.Unit (606 KB)
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