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3VGW
Biol. Unit 1
Info
Asym.Unit (180 KB)
Biol.Unit 1 (88 KB)
Biol.Unit 2 (89 KB)
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(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
[
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Hetero Components
(3, 14)
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
4
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
2
NVZ
4
Ligand/Ion
5-[(3AS,4S,6AR)-1-ACETYL-2-OXOHEXAHYDRO-1H-THIENO[3,4-D]IMIDAZOL-4-YL]PENTANOIC ACID
3
SO4
6
Ligand/Ion
SULFATE ION
[
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Sites
(14, 14)
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)
View:
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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
[
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SAPs(SNPs)/Variants
(1, 4)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_AVID_CHICK_001 (I34T, chain A/B/C/D, )
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
I
34
T
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(2, 6)
Info
All PROSITE Patterns/Profiles
1: AVIDIN_2 (A:2-123,C: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
2
A:2-123
C:2-123
-
-
2
AVIDIN_1
PS00577
Avidin-like domain signature.
AVID_CHICK
132-146
4
A:108-122
B:108-122
C:108-122
D:108-122
-
-
-
-
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
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:)
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Protein Domains
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)
(
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Organisms
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)
(
)
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:
[
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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
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Sorry, no Info available
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Chain C
Chain D
Asymmetric Unit 1
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select chains 'A' and 'C'
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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select non-helix/non-sheet protein parts
set fontsize 20
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Asym.Unit (180 KB)
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