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...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
3KAS
Asym. Unit
Info
Asym.Unit (282 KB)
Biol.Unit 1 (545 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
MACHUPO VIRUS GP1 BOUND TO HUMAN TRANSFERRIN RECEPTOR 1
Authors
:
J. Abraham, K. D. Corbett, S. C. Harrison
Date
:
19 Oct 09 (Deposition) - 09 Mar 10 (Release) - 15 Jun 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (2x)
Keywords
:
Machupo Virus, Transferrin Receptor 1, Arenavirus, Cell Membrane, Disulfide Bond, Endocytosis, Glycoprotein, Host-Virus Interaction, Receptor, Secreted, Transmembrane, Viral Protein-Endocytosis Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Abraham, K. D. Corbett, M. Farzan, H. Choe, S. C. Harrison
Structural Basis For Receptor Recognition By New World Hemorrhagic Fever Arenaviruses.
Nat. Struct. Mol. Biol. V. 17 438 2010
[
close entry info
]
Hetero Components
(6, 21)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
2a: ALPHA-L-FUCOSE (FUCa)
3a: POTASSIUM ION (Ka)
4a: ALPHA-D-MANNOSE (MANa)
4b: ALPHA-D-MANNOSE (MANb)
4c: ALPHA-D-MANNOSE (MANc)
4d: ALPHA-D-MANNOSE (MANd)
5a: N-ACETYL-D-GLUCOSAMINE (NAGa)
5b: N-ACETYL-D-GLUCOSAMINE (NAGb)
5c: N-ACETYL-D-GLUCOSAMINE (NAGc)
5d: N-ACETYL-D-GLUCOSAMINE (NAGd)
5e: N-ACETYL-D-GLUCOSAMINE (NAGe)
5f: N-ACETYL-D-GLUCOSAMINE (NAGf)
5g: N-ACETYL-D-GLUCOSAMINE (NAGg)
5h: N-ACETYL-D-GLUCOSAMINE (NAGh)
6a: PHOSPHATE ION (PO4a)
6b: PHOSPHATE ION (PO4b)
6c: PHOSPHATE ION (PO4c)
6d: PHOSPHATE ION (PO4d)
6e: PHOSPHATE ION (PO4e)
6f: PHOSPHATE ION (PO4f)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
1
Ligand/Ion
BETA-D-MANNOSE
2
FUC
1
Ligand/Ion
ALPHA-L-FUCOSE
3
K
1
Ligand/Ion
POTASSIUM ION
4
MAN
4
Ligand/Ion
ALPHA-D-MANNOSE
5
NAG
8
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
6
PO4
6
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
]
Sites
(21, 21)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HOH A:95 , ASN A:251
BINDING SITE FOR RESIDUE NAG A 1001
02
AC2
SOFTWARE
HOH A:55 , ASN A:727 , THR A:729 , HOH A:802
BINDING SITE FOR RESIDUE NAG A 1011
03
AC3
SOFTWARE
HOH A:87 , TYR A:123 , TRP A:124 , HIS A:603 , GLN B:238
BINDING SITE FOR RESIDUE PO4 A 2
04
AC4
SOFTWARE
ASP A:400 , HIS A:401 , LYS A:672 , LYS A:673 , ASP A:676 , ARG A:680 , HOH A:799 , HOH A:836
BINDING SITE FOR RESIDUE PO4 A 3
05
AC5
SOFTWARE
HOH A:107 , LYS A:495 , SER A:497 , SER A:554 , PHE A:555
BINDING SITE FOR RESIDUE PO4 A 4
06
AC6
SOFTWARE
TRP A:124 , ASN A:512 , HOH A:842
BINDING SITE FOR RESIDUE PO4 A 6
07
AC7
SOFTWARE
LEU A:122 , GLN A:443
BINDING SITE FOR RESIDUE K A 1
08
AC8
SOFTWARE
LYS A:439 , ASN B:95 , SER B:97
BINDING SITE FOR RESIDUE NAG B 1001
09
AC9
SOFTWARE
ASN B:137 , GLN B:219 , CYS B:220 , ASP B:222
BINDING SITE FOR RESIDUE NAG B 1011
10
BC1
SOFTWARE
ASN B:166 , THR B:168 , NAG B:1022 , FUC B:1023
BINDING SITE FOR RESIDUE NAG B 1021
11
BC2
SOFTWARE
NAG B:1021 , FUC B:1023
BINDING SITE FOR RESIDUE NAG B 1022
12
BC3
SOFTWARE
NAG B:1021 , NAG B:1022
BINDING SITE FOR RESIDUE FUC B 1023
13
BC4
SOFTWARE
LEU B:118 , ASN B:178 , SER B:180 , ASP B:184 , TYR B:214 , NAG B:1032
BINDING SITE FOR RESIDUE NAG B 1031
14
BC5
SOFTWARE
ALA B:182 , GLY B:210 , NAG B:1031 , BMA B:1033 , MAN B:1035 , MAN B:1037
BINDING SITE FOR RESIDUE NAG B 1032
15
BC6
SOFTWARE
PHE A:187 , NAG B:1032 , MAN B:1034 , MAN B:1035
BINDING SITE FOR RESIDUE BMA B 1033
16
BC7
SOFTWARE
GLU A:383 , BMA B:1033
BINDING SITE FOR RESIDUE MAN B 1034
17
BC8
SOFTWARE
GLN A:185 , NAG B:1032 , BMA B:1033 , MAN B:1036 , MAN B:1037
BINDING SITE FOR RESIDUE MAN B 1035
18
BC9
SOFTWARE
ASP B:183 , MAN B:1035
BINDING SITE FOR RESIDUE MAN B 1036
19
CC1
SOFTWARE
HOH A:854 , GLY B:210 , LYS B:211 , HOH B:263 , NAG B:1032 , MAN B:1035
BINDING SITE FOR RESIDUE MAN B 1037
20
CC2
SOFTWARE
ASP B:227 , GLY B:230 , VAL B:231 , ASN B:232 , HIS B:233
BINDING SITE FOR RESIDUE PO4 B 1
21
CC3
SOFTWARE
LYS B:190 , ARG B:193 , ARG B:197 , ASP B:205
BINDING SITE FOR RESIDUE PO4 B 5
[
close Site info
]
SAPs(SNPs)/Variants
(4, 4)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_012737 (S142S, chain A, )
2: VAR_051806 (L212V, chain A, )
3: VAR_051807 (G420S, chain A, )
4: VAR_051808 (R677H, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_012737
G
142
S
TFR1_HUMAN
Polymorphism
3817672
A
S
142
S
2
UniProt
VAR_051806
L
212
V
TFR1_HUMAN
Polymorphism
41301381
A
L
212
V
3
UniProt
VAR_051807
G
420
S
TFR1_HUMAN
Polymorphism
41295879
A
G
420
S
4
UniProt
VAR_051808
R
677
H
TFR1_HUMAN
Polymorphism
41298067
A
R
677
H
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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
(16, 16)
Info
All Exons
Exon 1.5 (A:121-145)
Exon 1.6 (A:145-195)
Exon 1.7b (A:195-229)
Exon 1.8b (A:230-267)
Exon 1.9 (A:268-300)
Exon 1.10b (A:301-347 (gaps))
Exon 1.11a (A:347-400)
Exon 1.12 (A:400-440)
Exon 1.14c (A:440-468)
Exon 1.14d (A:469-490)
Exon 1.15c (A:490-512)
Exon 1.16b (A:513-532)
Exon 1.17b (A:532-559)
Exon 1.18c (A:560-633)
Exon 1.19c (A:634-680)
Exon 1.20a (A:681-756)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.3/1.5
02: Boundary 1.5/1.6
03: Boundary 1.6/1.7b
04: Boundary 1.7b/1.8b
05: Boundary 1.8b/1.9
06: Boundary 1.9/1.10b
07: Boundary 1.10b/1.11a
08: Boundary 1.11a/1.12
09: Boundary 1.12/1.14c
10: Boundary 1.14c/1.14d
11: Boundary 1.14d/1.15c
12: Boundary 1.15c/1.16b
13: Boundary 1.16b/1.17b
14: Boundary 1.17b/1.18c
15: Boundary 1.18c/1.19c
16: Boundary 1.19c/1.20a
17: Boundary 1.20a/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1e
ENST00000392396
1e
ENSE00001511658
chr3:
195808961-195808702
260
TFR1_HUMAN
-
0
0
-
-
1.2
ENST00000392396
2
ENSE00002184017
chr3:
195803993-195803935
59
TFR1_HUMAN
1-12
12
0
-
-
1.3
ENST00000392396
3
ENSE00000336901
chr3:
195802231-195802030
202
TFR1_HUMAN
13-80
68
0
-
-
1.5
ENST00000392396
5
ENSE00001645063
chr3:
195800996-195800801
196
TFR1_HUMAN
80-145
66
1
A:121-145
25
1.6
ENST00000392396
6
ENSE00001615518
chr3:
195799023-195798874
150
TFR1_HUMAN
145-195
51
1
A:145-195
51
1.7b
ENST00000392396
7b
ENSE00000781814
chr3:
195798369-195798267
103
TFR1_HUMAN
195-229
35
1
A:195-229
35
1.8b
ENST00000392396
8b
ENSE00000336905
chr3:
195796439-195796326
114
TFR1_HUMAN
230-267
38
1
A:230-267
38
1.9
ENST00000392396
9
ENSE00000781817
chr3:
195795001-195794903
99
TFR1_HUMAN
268-300
33
1
A:268-300
33
1.10b
ENST00000392396
10b
ENSE00000781818
chr3:
195794528-195794389
140
TFR1_HUMAN
301-347
47
1
A:301-347 (gaps)
47
1.11a
ENST00000392396
11a
ENSE00000781819
chr3:
195792471-195792314
158
TFR1_HUMAN
347-400
54
1
A:347-400
54
1.12
ENST00000392396
12
ENSE00000781821
chr3:
195791299-195791180
120
TFR1_HUMAN
400-440
41
1
A:400-440
41
1.14c
ENST00000392396
14c
ENSE00001189905
chr3:
195789810-195789725
86
TFR1_HUMAN
440-468
29
1
A:440-468
29
1.14d
ENST00000392396
14d
ENSE00000781823
chr3:
195789516-195789453
64
TFR1_HUMAN
469-490
22
1
A:469-490
22
1.15c
ENST00000392396
15c
ENSE00000781824
chr3:
195787118-195787051
68
TFR1_HUMAN
490-512
23
1
A:490-512
23
1.16b
ENST00000392396
16b
ENSE00000781826
chr3:
195785503-195785445
59
TFR1_HUMAN
513-532
20
1
A:513-532
20
1.17b
ENST00000392396
17b
ENSE00000781827
chr3:
195785236-195785155
82
TFR1_HUMAN
532-559
28
1
A:532-559
28
1.18c
ENST00000392396
18c
ENSE00000781828
chr3:
195782172-195781951
222
TFR1_HUMAN
560-633
74
1
A:560-633
74
1.19c
ENST00000392396
19c
ENSE00000781829
chr3:
195780429-195780289
141
TFR1_HUMAN
634-680
47
1
A:634-680
47
1.20a
ENST00000392396
20a
ENSE00001405345
chr3:
195779055-195776347
2709
TFR1_HUMAN
681-760
80
1
A:681-756
76
[
close EXON info
]
SCOP Domains
(3, 3)
Info
All SCOP Domains
1a: SCOP_d3kasa3 (A:609-756)
2a: SCOP_d3kasa1 (A:121-189,A:383-608)
3a: SCOP_d3kasa2 (A:190-382)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
N-cbl like
(37)
Superfamily
:
Transferrin receptor-like dimerisation domain
(18)
Family
:
Transferrin receptor-like dimerisation domain
(18)
Protein domain
:
Transferrin receptor ectodomain, C-terminal domain
(4)
Human (Homo sapiens) [TaxId: 9606]
(4)
1a
d3kasa3
A:609-756
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Phosphorylase/hydrolase-like
(558)
Superfamily
:
Zn-dependent exopeptidases
(214)
Family
:
FolH catalytic domain-like
(18)
Protein domain
:
Transferrin receptor ectodomain, protease-like domain
(4)
Human (Homo sapiens) [TaxId: 9606]
(4)
2a
d3kasa1
A:121-189,A:383-608
Fold
:
The swivelling beta/beta/alpha domain
(136)
Superfamily
:
PA domain
(18)
Family
:
PA domain
(18)
Protein domain
:
Transferrin receptor ectodomain, apical domain
(4)
Human (Homo sapiens) [TaxId: 9606]
(4)
3a
d3kasa2
A:190-382
[
close SCOP info
]
CATH Domains
(3, 3)
Info
all CATH domains
1a: CATH_3kasA01 (A:121-194,A:380-613)
2a: CATH_3kasA02 (A:197-377)
3a: CATH_3kasA03 (A:614-755)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Aminopeptidase
(284)
Homologous Superfamily
:
Zn peptidases
(137)
Homo sapiens. Organism_taxid: 9606.
(1)
1a
3kasA01
A:121-194,A:380-613
Architecture
:
3-Layer(bba) Sandwich
(528)
Topology
:
Glucose Oxidase; domain 1
(52)
Homologous Superfamily
:
[code=3.50.30.30, no name defined]
(6)
Homo sapiens. Organism_taxid: 9606.
(1)
2a
3kasA02
A:197-377
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Transcription Elongation Factor S-II; Chain A
(14)
Homologous Superfamily
:
[code=1.20.930.40, no name defined]
(3)
Homo sapiens. Organism_taxid: 9606.
(1)
3a
3kasA03
A:614-755
[
close CATH info
]
Pfam Domains
(4, 4)
Info
all PFAM domains
1a: PFAM_Peptidase_M28_3kasA01 (A:400-579)
2a: PFAM_Arena_glycoprot_3kasB01 (B:86-241)
3a: PFAM_PA_3kasA02 (A:223-346)
4a: PFAM_TFR_dimer_3kasA03 (A:636-752)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Peptidase_MH
(119)
Family
:
Peptidase_M28
(38)
Homo sapiens (Human)
(30)
1a
Peptidase_M28-3kasA01
A:400-579
Clan
:
no clan defined [family: Arena_glycoprot]
(10)
Family
:
Arena_glycoprot
(10)
Machupo virus (MACV)
(2)
2a
Arena_glycoprot-3kasB01
B:86-241
Clan
:
no clan defined [family: PA]
(15)
Family
:
PA
(15)
Homo sapiens (Human)
(12)
3a
PA-3kasA02
A:223-346
Clan
:
no clan defined [family: TFR_dimer]
(12)
Family
:
TFR_dimer
(12)
Homo sapiens (Human)
(12)
4a
TFR_dimer-3kasA03
A:636-752
[
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 (282 KB)
Header - Asym.Unit
Biol.Unit 1 (545 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
3KAS
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
