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3CF1
Biol. Unit 1
Info
Asym.Unit (333 KB)
Biol.Unit 1 (639 KB)
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(1)
Title
:
STRUCTURE OF P97/VCP IN COMPLEX WITH ADP/ADP.ALFX
Authors
:
J. M. Davies, B. Delabarre, A. T. Brunger, W. I. Weis
Date
:
01 Mar 08 (Deposition) - 22 Apr 08 (Release) - 02 Jun 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
4.40
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (2x)
Keywords
:
Aaa, Cdc48, Erad, Atpase, Transport Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. M. Davies, A. T. Brunger, W. I. Weis
Improved Structures Of Full-Length P97, An Aaa Atpase: Implications For Mechanisms Of Nucleotide-Dependent Conformational Change.
Structure V. 16 715 2008
(for further references see the
PDB file header
)
[
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Hetero Components
(2, 18)
Info
All Hetero Components
1a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
1b: ADENOSINE-5'-DIPHOSPHATE (ADPb)
1c: ADENOSINE-5'-DIPHOSPHATE (ADPc)
1d: ADENOSINE-5'-DIPHOSPHATE (ADPd)
1e: ADENOSINE-5'-DIPHOSPHATE (ADPe)
1f: ADENOSINE-5'-DIPHOSPHATE (ADPf)
2a: ALUMINUM FLUORIDE (AF3a)
2b: ALUMINUM FLUORIDE (AF3b)
2c: ALUMINUM FLUORIDE (AF3c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ADP
12
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
AF3
6
Ligand/Ion
ALUMINUM FLUORIDE
[
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]
Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
9: AC9 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:205 , ILE A:206 , GLY A:207 , GLY A:248 , THR A:249 , GLY A:250 , LYS A:251 , THR A:252 , LEU A:253 , HIS A:384 , GLY A:408 , ALA A:409 , ARG C:359
BINDING SITE FOR RESIDUE ADP A 807
2
AC2
SOFTWARE
ASP A:478 , ILE A:479 , CYS A:522 , GLY A:523 , LYS A:524 , THR A:525 , LEU A:526 , ILE A:656 , GLY A:684 , ALA A:685 , THR A:688
BINDING SITE FOR RESIDUE ADP A 900
3
AC3
SOFTWARE
PRO A:519 , PRO A:520 , GLY A:521 , CYS A:522 , LYS A:524 , THR A:525
BINDING SITE FOR RESIDUE AF3 A 915
4
AC4
SOFTWARE
ARG A:359 , ASP B:205 , GLY B:207 , GLY B:248 , THR B:249 , GLY B:250 , LYS B:251 , THR B:252 , LEU B:253 , ASP B:304 , HIS B:384 , GLY B:408
BINDING SITE FOR RESIDUE ADP B 807
5
AC5
SOFTWARE
ASP B:478 , ILE B:479 , GLY B:521 , CYS B:522 , GLY B:523 , LYS B:524 , THR B:525 , LEU B:526 , ILE B:656 , ASN B:660 , GLY B:684 , ALA B:685 , THR B:688
BINDING SITE FOR RESIDUE ADP B 900
6
AC6
SOFTWARE
PRO B:519 , PRO B:520 , GLY B:521 , CYS B:522 , GLY B:523 , LYS B:524
BINDING SITE FOR RESIDUE AF3 B 915
7
AC7
SOFTWARE
ARG B:359 , ASP C:205 , ILE C:206 , GLY C:207 , PRO C:247 , GLY C:248 , THR C:249 , GLY C:250 , LYS C:251 , THR C:252 , LEU C:253 , HIS C:384 , GLY C:408 , ALA C:409
BINDING SITE FOR RESIDUE ADP C 807
8
AC8
SOFTWARE
ASP C:478 , ILE C:479 , GLY C:521 , CYS C:522 , GLY C:523 , LYS C:524 , THR C:525 , LEU C:526 , ILE C:656 , ASN C:660 , GLY C:684 , ALA C:685 , THR C:688
BINDING SITE FOR RESIDUE ADP C 900
9
AC9
SOFTWARE
PRO C:519 , PRO C:520 , GLY C:521 , CYS C:522 , GLY C:523 , LYS C:524
BINDING SITE FOR RESIDUE AF3 C 915
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 12)
Info
All PROSITE Patterns/Profiles
1: AAA (A:341-359,B:341-359,A:617-635,B:61...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
AAA
PS00674
AAA-protein family signature.
TERA_MOUSE
341-359
617-635
12
A:341-359
B:341-359
C:341-359
A:617-635
B:617-635
C:617-635
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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
(3, 12)
Info
All SCOP Domains
1a: SCOP_d3cf1a1 (A:21-106)
1b: SCOP_d3cf1b1 (B:21-106)
1c: SCOP_d3cf1c1 (C:21-106)
2a: SCOP_d3cf1a4 (A:107-200)
2b: SCOP_d3cf1b4 (B:107-200)
2c: SCOP_d3cf1c4 (C:107-200)
3a: SCOP_d3cf1a2 (A:201-470)
3b: SCOP_d3cf1a3 (A:471-763)
3c: SCOP_d3cf1b2 (B:201-470)
3d: SCOP_d3cf1b3 (B:471-763)
3e: SCOP_d3cf1c2 (C:201-470)
3f: SCOP_d3cf1c3 (C:471-763)
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Classes
(
)
(
)
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(
)
(
)
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(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Double psi beta-barrel
(111)
Superfamily
:
ADC-like
(88)
Family
:
Cdc48 N-terminal domain-like
(16)
Protein domain
:
Membrane fusion ATPase p97 N-terminal domain , P97-Nn
(10)
Mouse (Mus musculus) [TaxId: 10090]
(5)
1a
d3cf1a1
A:21-106
1b
d3cf1b1
B:21-106
1c
d3cf1c1
C:21-106
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Cdc48 domain 2-like
(22)
Superfamily
:
Cdc48 domain 2-like
(22)
Family
:
Cdc48 domain 2-like
(16)
Protein domain
:
Membrane fusion atpase p97 domain 2, P97-Nc
(10)
Mouse (Mus musculus) [TaxId: 10090]
(5)
2a
d3cf1a4
A:107-200
2b
d3cf1b4
B:107-200
2c
d3cf1c4
C:107-200
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Superfamily
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Family
:
Extended AAA-ATPase domain
(92)
Protein domain
:
Membrane fusion ATPase VCP/p97
(4)
Mouse (Mus musculus) [TaxId: 10090]
(4)
3a
d3cf1a2
A:201-470
3b
d3cf1a3
A:471-763
3c
d3cf1b2
B:201-470
3d
d3cf1b3
B:471-763
3e
d3cf1c2
C:201-470
3f
d3cf1c3
C:471-763
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(0, 0)
Info
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Sorry, no Info available
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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
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Asym.Unit (333 KB)
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Header - Biol.Unit 1
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