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.
3VGW
Asym. Unit
Info
Asym.Unit (180 KB)
Biol.Unit 1 (88 KB)
Biol.Unit 2 (89 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 MONOAC-BIOTIN-AVIDIN COMPLEX
Authors
:
T. Terai, E. Maki, S. Sugiyama, Y. Takahashi, H. Matsumura, Y. Mori, T. N
Date
:
21 Aug 11 (Deposition) - 28 Dec 11 (Release) - 28 Dec 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.60
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Keywords
:
Beta Barrel, Biotin-Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Terai, E. Maki, S. Sugiyama, Y. Takahashi, H. Matsumura, Y. Mori, T. Nagano
Rational Development Of Caged-Biotin Protein-Labeling Agent And Some Applications In Live Cells
Chem. Biol. V. 18 1261 2011
[
close entry info
]
Hetero Components
(3, 28)
Info
All Hetero Components
1a: N-ACETYL-D-GLUCOSAMINE (NAGa)
1b: N-ACETYL-D-GLUCOSAMINE (NAGb)
1c: N-ACETYL-D-GLUCOSAMINE (NAGc)
1d: N-ACETYL-D-GLUCOSAMINE (NAGd)
1e: N-ACETYL-D-GLUCOSAMINE (NAGe)
1f: N-ACETYL-D-GLUCOSAMINE (NAGf)
1g: N-ACETYL-D-GLUCOSAMINE (NAGg)
1h: N-ACETYL-D-GLUCOSAMINE (NAGh)
2a: 5-[(3AS,4S,6AR)-1-ACETYL-2-OXOHEXA... (NVZa)
2b: 5-[(3AS,4S,6AR)-1-ACETYL-2-OXOHEXA... (NVZb)
2c: 5-[(3AS,4S,6AR)-1-ACETYL-2-OXOHEXA... (NVZc)
2d: 5-[(3AS,4S,6AR)-1-ACETYL-2-OXOHEXA... (NVZd)
2e: 5-[(3AS,4S,6AR)-1-ACETYL-2-OXOHEXA... (NVZe)
2f: 5-[(3AS,4S,6AR)-1-ACETYL-2-OXOHEXA... (NVZf)
2g: 5-[(3AS,4S,6AR)-1-ACETYL-2-OXOHEXA... (NVZg)
2h: 5-[(3AS,4S,6AR)-1-ACETYL-2-OXOHEXA... (NVZh)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
3f: SULFATE ION (SO4f)
3g: SULFATE ION (SO4g)
3h: SULFATE ION (SO4h)
3i: SULFATE ION (SO4i)
3j: SULFATE ION (SO4j)
3k: SULFATE ION (SO4k)
3l: SULFATE ION (SO4l)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAG
8
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
2
NVZ
8
Ligand/Ion
5-[(3AS,4S,6AR)-1-ACETYL-2-OXOHEXAHYDRO-1H-THIENO[3,4-D]IMIDAZOL-4-YL]PENTANOIC ACID
3
SO4
12
Ligand/Ion
SULFATE ION
[
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
ASN A:12 , LEU A:14 , SER A:16 , TYR A:33 , THR A:35 , VAL A:37 , THR A:38 , ALA A:39 , TRP A:70 , PHE A:72 , SER A:73 , SER A:75 , THR A:77 , TRP A:97 , ASN A:118 , HOH A:143 , TRP C:110
BINDING SITE FOR RESIDUE NVZ A 1124
02
AC2
SOFTWARE
LYS A:9 , GLY A:15 , ASN A:17
BINDING SITE FOR RESIDUE NAG A 1125
03
AC3
SOFTWARE
ARG A:2 , LYS A:90 , GLU A:91 , ARG A:122 , HOH A:253
BINDING SITE FOR RESIDUE SO4 A 1126
04
AC4
SOFTWARE
ARG A:59 , THR A:60 , HOH A:157
BINDING SITE FOR RESIDUE SO4 A 1127
05
AC5
SOFTWARE
ASN B:12 , LEU B:14 , SER B:16 , TYR B:33 , THR B:35 , VAL B:37 , THR B:38 , ALA B:39 , THR B:40 , TRP B:70 , SER B:73 , SER B:75 , THR B:77 , TRP B:97 , ASN B:118 , HOH B:487 , TRP D:110
BINDING SITE FOR RESIDUE NVZ B 1124
06
AC6
SOFTWARE
GLY B:15 , ASN B:17 , ILE B:34 , LEU B:123
BINDING SITE FOR RESIDUE NAG B 1125
07
AC7
SOFTWARE
ARG B:59 , THR B:60 , HOH B:553
BINDING SITE FOR RESIDUE SO4 B 1126
08
AC8
SOFTWARE
TRP A:110 , ASN C:12 , LEU C:14 , SER C:16 , TYR C:33 , THR C:35 , VAL C:37 , THR C:38 , ALA C:39 , THR C:40 , TRP C:70 , PHE C:72 , SER C:73 , SER C:75 , THR C:77 , TRP C:97 , ASN C:118 , HOH C:388 , HOH C:480
BINDING SITE FOR RESIDUE NVZ C 1124
09
AC9
SOFTWARE
LYS C:9 , GLY C:15 , ASN C:17 , LEU C:123
BINDING SITE FOR RESIDUE NAG C 1125
10
BC1
SOFTWARE
ARG C:2 , LYS C:90 , GLU C:91 , ARG C:122 , HOH C:129
BINDING SITE FOR RESIDUE SO4 C 1126
11
BC2
SOFTWARE
ARG C:59 , THR C:60 , HOH C:138
BINDING SITE FOR RESIDUE SO4 C 1127
12
BC3
SOFTWARE
TRP B:110 , ASN D:12 , LEU D:14 , SER D:16 , TYR D:33 , THR D:35 , VAL D:37 , THR D:38 , ALA D:39 , THR D:40 , TRP D:70 , PHE D:72 , SER D:73 , SER D:75 , THR D:77 , TRP D:97 , ASN D:118
BINDING SITE FOR RESIDUE NVZ D 1124
13
BC4
SOFTWARE
GLY D:15 , ASN D:17
BINDING SITE FOR RESIDUE NAG D 1125
14
BC5
SOFTWARE
ARG D:59 , THR D:60 , HOH D:283
BINDING SITE FOR RESIDUE SO4 D 1126
15
BC6
SOFTWARE
ASN E:12 , LEU E:14 , SER E:16 , TYR E:33 , THR E:35 , VAL E:37 , ALA E:39 , THR E:40 , TRP E:70 , PHE E:72 , SER E:73 , SER E:75 , THR E:77 , TRP E:97 , ASN E:118 , HOH E:347 , TRP G:110
BINDING SITE FOR RESIDUE NVZ E 1124
16
BC7
SOFTWARE
LYS E:9 , GLY E:15 , ASN E:17 , LEU E:123
BINDING SITE FOR RESIDUE NAG E 1125
17
BC8
SOFTWARE
ARG E:2 , LYS E:90 , GLU E:91 , ARG E:122 , HOH E:127
BINDING SITE FOR RESIDUE SO4 E 1126
18
BC9
SOFTWARE
ARG E:59 , THR E:60
BINDING SITE FOR RESIDUE SO4 E 1127
19
CC1
SOFTWARE
ASN F:12 , LEU F:14 , SER F:16 , TYR F:33 , THR F:35 , VAL F:37 , THR F:38 , ALA F:39 , THR F:40 , TRP F:70 , SER F:73 , SER F:75 , THR F:77 , TRP F:97 , ASN F:118 , HOH F:246 , TRP H:110
BINDING SITE FOR RESIDUE NVZ F 1124
20
CC2
SOFTWARE
GLY F:15 , ASN F:17 , ILE F:34 , LEU F:123
BINDING SITE FOR RESIDUE NAG F 1125
21
CC3
SOFTWARE
ARG F:59 , THR F:60 , HOH F:138
BINDING SITE FOR RESIDUE SO4 F 1126
22
CC4
SOFTWARE
TRP E:110 , ASN G:12 , LEU G:14 , SER G:16 , TYR G:33 , THR G:35 , VAL G:37 , THR G:38 , ALA G:39 , THR G:40 , TRP G:70 , PHE G:72 , SER G:73 , SER G:75 , THR G:77 , TRP G:97 , ASN G:118 , HOH G:463 , HOH G:514
BINDING SITE FOR RESIDUE NVZ G 1124
23
CC5
SOFTWARE
LYS G:9 , GLY G:15 , ASN G:17 , LEU G:123 , HOH G:438
BINDING SITE FOR RESIDUE NAG G 1125
24
CC6
SOFTWARE
ARG G:2 , LYS G:90 , GLU G:91 , ARG G:122 , HOH G:130 , HOH G:135
BINDING SITE FOR RESIDUE SO4 G 1126
25
CC7
SOFTWARE
ARG G:59 , THR G:60 , HOH G:225
BINDING SITE FOR RESIDUE SO4 G 1127
26
CC8
SOFTWARE
TRP F:110 , ASN H:12 , LEU H:14 , SER H:16 , TYR H:33 , THR H:35 , VAL H:37 , THR H:38 , ALA H:39 , THR H:40 , TRP H:70 , SER H:73 , SER H:75 , THR H:77 , TRP H:97 , ASN H:118
BINDING SITE FOR RESIDUE NVZ H 1124
27
CC9
SOFTWARE
LYS H:9 , GLY H:15 , ASN H:17 , LEU H:123
BINDING SITE FOR RESIDUE NAG H 1125
28
DC1
SOFTWARE
ARG H:59 , THR H:60
BINDING SITE FOR RESIDUE SO4 H 1126
[
close Site info
]
SAPs(SNPs)/Variants
(1, 8)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_AVID_CHICK_001 (I34T, chain A/B/C/D/E/F/G/H, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_AVID_CHICK_001
*
I
58
T
AVID_CHICK
---
---
A/B/C/D/E/F/G/H
I
34
T
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 12)
Info
All PROSITE Patterns/Profiles
1: AVIDIN_2 (A:2-123,C:2-123,E:2-123,G:2-123)
2: AVIDIN_1 (A:108-122,B:108-122,C:108-122,D:10...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
AVIDIN_2
PS51326
Avidin-like domain profile.
AVID_CHICK
26-149
4
A:2-123
C:2-123
E:2-123
G:2-123
2
AVIDIN_1
PS00577
Avidin-like domain signature.
AVID_CHICK
132-146
8
A:108-122
B:108-122
C:108-122
D:108-122
E:108-122
F:108-122
G:108-122
H:108-122
[
close PROSITE info
]
Exons
(4, 32)
Info
All Exons
Exon 1.1 (A:1-3 | B:3-3 | C:1-3 | D:3-3 | E:...)
Exon 1.4 (A:4-74 | B:4-74 | C:4-74 | D:4-74 ...)
Exon 1.5 (A:74-114 | B:74-114 | C:74-114 | D...)
Exon 1.6a (A:114-123 | B:114-123 | C:114-123 ...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/1.4
3: Boundary 1.4/1.5
4: Boundary 1.5/1.6a
5: Boundary 1.6a/-
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
1.1
ENSGALT00000003855
1
ENSGALE00000024242
Z:8485802-8485882
81
AVID_CHICK
1-27
27
8
A:1-3
B:3-3
C:1-3
D:3-3
E:1-3
F:3-3
G:1-3
H:3-3
3
1
3
1
3
1
3
1
1.4
ENSGALT00000003855
4
ENSGALE00000024240
Z:8501440-8501650
211
AVID_CHICK
28-98
71
8
A:4-74
B:4-74
C:4-74
D:4-74
E:4-74
F:4-74
G:4-74
H:4-74
71
71
71
71
71
71
71
71
1.5
ENSGALT00000003855
5
ENSGALE00000024243
Z:8502076-8502196
121
AVID_CHICK
98-138
41
8
A:74-114
B:74-114
C:74-114
D:74-114
E:74-114
F:74-114
G:74-114
H:74-114
41
41
41
41
41
41
41
41
1.6a
ENSGALT00000003855
6a
ENSGALE00000024241
Z:8502284-8502409
126
AVID_CHICK
138-152
15
8
A:114-123
B:114-123
C:114-123
D:114-123
E:114-123
F:114-123
G:114-123
H:114-123
10
10
10
10
10
10
10
10
[
close EXON info
]
SCOP Domains
(1, 8)
Info
All SCOP Domains
1a: SCOP_d3vgwa_ (A:)
1b: SCOP_d3vgwb_ (B:)
1c: SCOP_d3vgwc_ (C:)
1d: SCOP_d3vgwd_ (D:)
1e: SCOP_d3vgwe_ (E:)
1f: SCOP_d3vgwf_ (F:)
1g: SCOP_d3vgwg_ (G:)
1h: SCOP_d3vgwh_ (H:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Streptavidin-like
(225)
Superfamily
:
Avidin/streptavidin
(197)
Family
:
Avidin/streptavidin
(181)
Protein domain
:
automated matches
(50)
Chicken (Gallus gallus) [TaxId: 9031]
(23)
1a
d3vgwa_
A:
1b
d3vgwb_
B:
1c
d3vgwc_
C:
1d
d3vgwd_
D:
1e
d3vgwe_
E:
1f
d3vgwf_
F:
1g
d3vgwg_
G:
1h
d3vgwh_
H:
[
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 (180 KB)
Header - Asym.Unit
Biol.Unit 1 (88 KB)
Header - Biol.Unit 1
Biol.Unit 2 (89 KB)
Header - Biol.Unit 2
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
3VGW
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help