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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.
3VHM
Asym. Unit
Info
Asym.Unit (93 KB)
Biol.Unit 1 (87 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF NPC-BIOTIN-AVIDIN COMPLEX
Authors
:
T. Terai, E. Maki, S. Sugiyama, Y. Takahashi, H. Matsumura, Y. Mori, T. N
Date
:
29 Aug 11 (Deposition) - 28 Dec 11 (Release) - 28 Dec 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (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
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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)
2a: 5-[(3AS,4R,6AR)-1-{[(1R)-1-(6-NITR... (NPKa)
2b: 5-[(3AS,4R,6AR)-1-{[(1R)-1-(6-NITR... (NPKb)
2c: 5-[(3AS,4R,6AR)-1-{[(1R)-1-(6-NITR... (NPKc)
2d: 5-[(3AS,4R,6AR)-1-{[(1R)-1-(6-NITR... (NPKd)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
3f: SULFATE ION (SO4f)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAG
4
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
2
NPK
4
Ligand/Ion
5-[(3AS,4R,6AR)-1-{[(1R)-1-(6-NITRO-1,3-BENZODIOXOL-5-YL)ETHOXY]CARBONYL}-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:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:12 , ASP A:13 , LEU A:14 , SER A:16 , TYR A:33 , THR A:35 , VAL A:37 , THR A:38 , ALA A:39 , TRP A:70 , SER A:73 , SER A:75 , TRP A:97 , ILE A:117 , ASN A:118 , HOH A:124 , GLY C:107 , TRP C:110 , HOH C:159
BINDING SITE FOR RESIDUE NPK A 1124
02
AC2
SOFTWARE
LYS A:9 , GLY A:15 , ASN A:17 , ILE A:34 , LEU A:123
BINDING SITE FOR RESIDUE NAG A 1125
03
AC3
SOFTWARE
ARG A:2 , LYS A:90 , GLU A:91 , ARG A:122 , HOH A:138 , LYS D:9 , HOH D:173
BINDING SITE FOR RESIDUE SO4 A 1126
04
AC4
SOFTWARE
ARG A:59 , THR A:60
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 , TRP B:70 , SER B:73 , SER B:75 , TRP B:97 , ILE B:117 , ASN B:118 , ILE B:119 , HOH B:142 , HOH B:194 , TRP D:110
BINDING SITE FOR RESIDUE NPK B 1124
06
AC6
SOFTWARE
GLY B:15 , ASN B:17 , ILE B:34
BINDING SITE FOR RESIDUE NAG B 1125
07
AC7
SOFTWARE
LYS B:9 , ARG C:2 , LYS C:90 , GLU C:91 , ARG C:122 , HOH C:149 , HOH C:185
BINDING SITE FOR RESIDUE SO4 B 1126
08
AC8
SOFTWARE
ARG B:59 , THR B:60 , ARG D:87
BINDING SITE FOR RESIDUE SO4 B 1127
09
AC9
SOFTWARE
GLY A:107 , TRP A:110 , ASN C:12 , LEU C:14 , SER C:16 , TYR C:33 , THR C:35 , THR C:38 , ALA C:39 , THR C:40 , TRP C:70 , SER C:75 , TRP C:97 , LEU C:99 , ILE C:117 , ASN C:118 , HOH C:181
BINDING SITE FOR RESIDUE NPK C 1124
10
BC1
SOFTWARE
GLY C:15 , ASN C:17
BINDING SITE FOR RESIDUE NAG C 1125
11
BC2
SOFTWARE
ARG C:59 , THR C:60 , HOH C:154
BINDING SITE FOR RESIDUE SO4 C 1127
12
BC3
SOFTWARE
TRP B:110 , ASN D:12 , ASP D:13 , LEU D:14 , SER D:16 , TYR D:33 , THR D:35 , VAL D:37 , THR D:38 , ALA D:39 , TRP D:70 , SER D:73 , SER D:75 , TRP D:97 , ILE D:117 , ASN D:118 , ILE D:119 , HOH D:139 , HOH D:167
BINDING SITE FOR RESIDUE NPK D 1124
13
BC4
SOFTWARE
GLY D:15 , ASN D:17 , ILE D:34
BINDING SITE FOR RESIDUE NAG D 1125
14
BC5
SOFTWARE
ARG D:59 , THR D:60 , HOH D:152
BINDING SITE FOR RESIDUE SO4 D 1126
[
close Site info
]
SAPs(SNPs)/Variants
(1, 4)
Info
(mutated residues are not available)
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)
[
close SNP/Variant info
]
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
[
close PROSITE info
]
Exons
(4, 16)
Info
All Exons
Exon 1.1 (A:1-3 | B:3-3 | C:1-3 | D:3-3)
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:
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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
4
A:1-3
B:3-3
C:1-3
D:3-3
3
1
3
1
1.4
ENSGALT00000003855
4
ENSGALE00000024240
Z:8501440-8501650
211
AVID_CHICK
28-98
71
4
A:4-74
B:4-74
C:4-74
D:4-74
71
71
71
71
1.5
ENSGALT00000003855
5
ENSGALE00000024243
Z:8502076-8502196
121
AVID_CHICK
98-138
41
4
A:74-114
B:74-114
C:74-114
D:74-114
41
41
41
41
1.6a
ENSGALT00000003855
6a
ENSGALE00000024241
Z:8502284-8502409
126
AVID_CHICK
138-152
15
4
A:114-123
B:114-123
C:114-123
D:114-123
10
10
10
10
[
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SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d3vhma_ (A:)
1b: SCOP_d3vhmb_ (B:)
1c: SCOP_d3vhmc_ (C:)
1d: SCOP_d3vhmd_ (D:)
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Protein Domains
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(
)
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
d3vhma_
A:
1b
d3vhmb_
B:
1c
d3vhmc_
C:
1d
d3vhmd_
D:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
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Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Asymmetric Unit 1
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select residue range 5 to 10 in chain 'A'
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