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3CF1
Asym. Unit
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, 9)
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
6
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
AF3
3
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:
Select:
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 not available)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 6)
Info
All PROSITE Patterns/Profiles
1: AAA (A:341-359,B:341-359,C:341-359|A: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
6
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
View:
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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)
View:
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(
)
(
)
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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
View:
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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
Asymmetric Unit 1
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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
show bonds with a radius of 100 units (=0.4Å)
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Asym.Unit (333 KB)
Header - Asym.Unit
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Header - Biol.Unit 1
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