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1S3S
Asym. Unit
Info
Asym.Unit (430 KB)
Biol.Unit 1 (419 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF AAA ATPASE P97/VCP ND1 IN COMPLEX WITH P47 C
Authors
:
I. Dreveny, H. Kondo, K. Uchiyama, A. Shaw, X. Zhang, P. S. Freemont
Date
:
14 Jan 04 (Deposition) - 30 Mar 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.90
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I
Biol. Unit 1: A,B,C,D,E,F,G,H,I (1x)
Keywords
:
Aaa Atpase, P97, P47, Protein-Protein Complex, Ubx Domain, Protein Binding
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
I. Dreveny, H. Kondo, K. Uchiyama, A. Shaw, X. Zhang, P. S. Freemont
Structural Basis Of The Interaction Between The Aaa Atpase P97/Vcp And Its Adaptor Protein P47.
Embo J. V. 23 1030 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 6)
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)
View:
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Label:
No.
Name
Count
Type
Full Name
1
ADP
6
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
[
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]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:205 , GLY A:207 , GLY A:248 , THR A:249 , GLY A:250 , LYS A:251 , THR A:252 , LEU A:253 , ILE A:380 , HIS A:384 , GLY A:408 , ALA A:409 , HOH A:808
BINDING SITE FOR RESIDUE ADP A 800
2
AC2
SOFTWARE
ASP B:205 , VAL B:206 , GLY B:207 , GLY B:248 , THR B:249 , GLY B:250 , LYS B:251 , THR B:252 , LEU B:253 , ILE B:380 , HIS B:384 , GLY B:408 , ALA B:409 , ARG F:359
BINDING SITE FOR RESIDUE ADP B 801
3
AC3
SOFTWARE
ASP C:205 , VAL C:206 , GLY C:207 , GLY C:248 , THR C:249 , GLY C:250 , LYS C:251 , THR C:252 , LEU C:253 , ILE C:380 , HIS C:384 , GLY C:408 , ALA C:409 , HOH C:803 , ARG D:359
BINDING SITE FOR RESIDUE ADP C 802
4
AC4
SOFTWARE
ASP D:205 , GLY D:207 , GLY D:248 , THR D:249 , GLY D:250 , LYS D:251 , THR D:252 , LEU D:253 , HIS D:384 , GLY D:408 , ALA D:409 , ALA D:412
BINDING SITE FOR RESIDUE ADP D 803
5
AC5
SOFTWARE
ARG C:359 , ASP E:205 , GLY E:207 , GLY E:248 , THR E:249 , GLY E:250 , LYS E:251 , THR E:252 , LEU E:253 , ILE E:380 , HIS E:384 , GLY E:408 , ALA E:409
BINDING SITE FOR RESIDUE ADP E 804
6
AC6
SOFTWARE
ASP F:205 , GLY F:207 , GLY F:248 , THR F:249 , GLY F:250 , LYS F:251 , THR F:252 , LEU F:253 , ILE F:380 , HIS F:384 , GLY F:408 , ALA F:409 , HOH F:810
BINDING SITE FOR RESIDUE ADP F 805
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 9)
Info
All PROSITE Patterns/Profiles
1: UBX (G:291-368,H:291-368,I:314-326)
2: AAA (A:341-359,B:341-359,C:341-359,D:34...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
UBX
PS50033
UBX domain profile.
NSF1C_RAT
291-368
3
G:291-368
H:291-368
I:314-326
2
AAA
PS00674
AAA-protein family signature.
TERA_MOUSE
341-359
617-635
6
A:341-359
B:341-359
C:341-359
D:341-359
E:341-359
F:341-359
-
[
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Exons
(3, 8)
Info
All Exons
Exon 1.8 (G:253-262 | H:257-262 | -)
Exon 1.9 (G:262-317 | H:262-317 (gaps) | I:2...)
Exon 1.10 (G:317-370 | H:317-370 | I:317-326)
View:
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All Exon Boundaries
1: Boundary 1.7/1.8
2: Boundary 1.8/1.9
3: Boundary 1.9/1.10
4: Boundary 1.10/-
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
ENSRNOT00000011654
1
ENSRNOE00000080778
chr3:
141799286-141799498
213
NSF1C_RAT
1-35
35
0
-
-
1.2
ENSRNOT00000011654
2
ENSRNOE00000080974
chr3:
141801645-141801742
98
NSF1C_RAT
36-68
33
0
-
-
1.3
ENSRNOT00000011654
3
ENSRNOE00000081202
chr3:
141806924-141806998
75
NSF1C_RAT
68-93
26
0
-
-
1.5
ENSRNOT00000011654
5
ENSRNOE00000081435
chr3:
141809288-141809453
166
NSF1C_RAT
93-148
56
0
-
-
1.6
ENSRNOT00000011654
6
ENSRNOE00000081642
chr3:
141810321-141810413
93
NSF1C_RAT
149-179
31
0
-
-
1.7
ENSRNOT00000011654
7
ENSRNOE00000081878
chr3:
141811633-141811742
110
NSF1C_RAT
180-216
37
0
-
-
1.8
ENSRNOT00000011654
8
ENSRNOE00000082111
chr3:
141812671-141812808
138
NSF1C_RAT
216-262
47
2
G:253-262
H:257-262
-
10
6
-
1.9
ENSRNOT00000011654
9
ENSRNOE00000082354
chr3:
141821967-141822131
165
NSF1C_RAT
262-317
56
3
G:262-317
H:262-317 (gaps)
I:277-317 (gaps)
56
56
41
1.10
ENSRNOT00000011654
10
ENSRNOE00000349261
chr3:
141823371-141823731
361
NSF1C_RAT
317-370
54
3
G:317-370
H:317-370
I:317-326
54
54
10
[
close EXON info
]
SCOP Domains
(4, 21)
Info
All SCOP Domains
1a: SCOP_d1s3sa1 (A:23-106)
1b: SCOP_d1s3se1 (E:23-106)
1c: SCOP_d1s3sf1 (F:18-106)
1d: SCOP_d1s3sb1 (B:23-106)
1e: SCOP_d1s3sc1 (C:22-106)
1f: SCOP_d1s3sd1 (D:23-106)
2a: SCOP_d1s3sg_ (G:)
2b: SCOP_d1s3sh_ (H:)
2c: SCOP_d1s3si_ (I:)
3a: SCOP_d1s3sa3 (A:107-200)
3b: SCOP_d1s3se3 (E:107-200)
3c: SCOP_d1s3sf3 (F:107-200)
3d: SCOP_d1s3sb3 (B:107-200)
3e: SCOP_d1s3sc3 (C:107-200)
3f: SCOP_d1s3sd3 (D:107-200)
4a: SCOP_d1s3sa2 (A:201-458)
4b: SCOP_d1s3sb2 (B:201-458)
4c: SCOP_d1s3sc2 (C:201-458)
4d: SCOP_d1s3sd2 (D:201-458)
4e: SCOP_d1s3se2 (E:201-458)
4f: SCOP_d1s3sf2 (F:201-458)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
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
d1s3sa1
A:23-106
1b
d1s3se1
E:23-106
1c
d1s3sf1
F:18-106
1d
d1s3sb1
B:23-106
1e
d1s3sc1
C:22-106
1f
d1s3sd1
D:23-106
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
beta-Grasp (ubiquitin-like)
(1032)
Superfamily
:
Ubiquitin-like
(546)
Family
:
UBX domain
(13)
Protein domain
:
p47
(3)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(3)
2a
d1s3sg_
G:
2b
d1s3sh_
H:
2c
d1s3si_
I:
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)
3a
d1s3sa3
A:107-200
3b
d1s3se3
E:107-200
3c
d1s3sf3
F:107-200
3d
d1s3sb3
B:107-200
3e
d1s3sc3
C:107-200
3f
d1s3sd3
D: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)
4a
d1s3sa2
A:201-458
4b
d1s3sb2
B:201-458
4c
d1s3sc2
C:201-458
4d
d1s3sd2
D:201-458
4e
d1s3se2
E:201-458
4f
d1s3sf2
F:201-458
[
close SCOP info
]
CATH Domains
(5, 26)
Info
all CATH domains
1a: CATH_1s3sA02 (A:199-370)
1b: CATH_1s3sB02 (B:199-370)
1c: CATH_1s3sC02 (C:199-370)
1d: CATH_1s3sD02 (D:199-370)
1e: CATH_1s3sE02 (E:199-370)
1f: CATH_1s3sF02 (F:199-370)
2a: CATH_1s3sH00 (H:257-370)
2b: CATH_1s3sG00 (G:253-370)
3a: CATH_1s3sA03 (A:109-185)
3b: CATH_1s3sB03 (B:109-185)
3c: CATH_1s3sC03 (C:109-185)
3d: CATH_1s3sD03 (D:109-185)
3e: CATH_1s3sE03 (E:109-185)
3f: CATH_1s3sF03 (F:109-185)
4a: CATH_1s3sA04 (A:372-458)
4b: CATH_1s3sB04 (B:372-458)
4c: CATH_1s3sC04 (C:372-458)
4d: CATH_1s3sD04 (D:372-458)
4e: CATH_1s3sE04 (E:372-458)
4f: CATH_1s3sF04 (F:372-458)
5a: CATH_1s3sF01 (F:21-107)
5b: CATH_1s3sC01 (C:22-107)
5c: CATH_1s3sA01 (A:23-107)
5d: CATH_1s3sB01 (B:23-107)
5e: CATH_1s3sD01 (D:23-107)
5f: CATH_1s3sE01 (E:23-107)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
P-loop containing nucleotide triphosphate hydrolases
(1378)
House mouse (Mus musculus)
(47)
1a
1s3sA02
A:199-370
1b
1s3sB02
B:199-370
1c
1s3sC02
C:199-370
1d
1s3sD02
D:199-370
1e
1s3sE02
E:199-370
1f
1s3sF02
F:199-370
Architecture
:
Roll
(3276)
Topology
:
Ubiquitin-like (UB roll)
(674)
Homologous Superfamily
:
Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
(286)
House mouse (Mus musculus)
(21)
2a
1s3sH00
H:257-370
2b
1s3sG00
G:253-370
Topology
:
Vcp-like ATPase; Chain A, domain 2
(12)
Homologous Superfamily
:
[code=3.10.330.10, no name defined]
(10)
House mouse (Mus musculus)
(5)
3a
1s3sA03
A:109-185
3b
1s3sB03
B:109-185
3c
1s3sC03
C:109-185
3d
1s3sD03
D:109-185
3e
1s3sE03
E:109-185
3f
1s3sF03
F:109-185
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Helicase, Ruva Protein; domain 3
(218)
Homologous Superfamily
:
[code=1.10.8.60, no name defined]
(73)
House mouse (Mus musculus)
(4)
4a
1s3sA04
A:372-458
4b
1s3sB04
B:372-458
4c
1s3sC04
C:372-458
4d
1s3sD04
D:372-458
4e
1s3sE04
E:372-458
4f
1s3sF04
F:372-458
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Barwin-like endoglucanases
(75)
Homologous Superfamily
:
[code=2.40.40.20, no name defined]
(63)
House mouse (Mus musculus)
(5)
5a
1s3sF01
F:21-107
5b
1s3sC01
C:22-107
5c
1s3sA01
A:23-107
5d
1s3sB01
B:23-107
5e
1s3sD01
D:23-107
5f
1s3sE01
E:23-107
[
close CATH info
]
Pfam Domains
(4, 21)
Info
all PFAM domains
1a: PFAM_CDC48_2_1s3sF01 (F:125-191)
1b: PFAM_CDC48_2_1s3sF02 (F:125-191)
1c: PFAM_CDC48_2_1s3sF03 (F:125-191)
1d: PFAM_CDC48_2_1s3sF04 (F:125-191)
1e: PFAM_CDC48_2_1s3sF05 (F:125-191)
1f: PFAM_CDC48_2_1s3sF06 (F:125-191)
2a: PFAM_AAA_1s3sF07 (F:241-371)
2b: PFAM_AAA_1s3sF08 (F:241-371)
2c: PFAM_AAA_1s3sF09 (F:241-371)
2d: PFAM_AAA_1s3sF10 (F:241-371)
2e: PFAM_AAA_1s3sF11 (F:241-371)
2f: PFAM_AAA_1s3sF12 (F:241-371)
3a: PFAM_UBX_1s3sI01 (I:314-326)
3b: PFAM_UBX_1s3sI02 (I:314-326)
3c: PFAM_UBX_1s3sI03 (I:314-326)
4a: PFAM_CDC48_N_1s3sF13 (F:25-108)
4b: PFAM_CDC48_N_1s3sF14 (F:25-108)
4c: PFAM_CDC48_N_1s3sF15 (F:25-108)
4d: PFAM_CDC48_N_1s3sF16 (F:25-108)
4e: PFAM_CDC48_N_1s3sF17 (F:25-108)
4f: PFAM_CDC48_N_1s3sF18 (F:25-108)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Cdc48_2-like
(11)
Family
:
CDC48_2
(8)
Mus musculus (Mouse)
(3)
1a
CDC48_2-1s3sF01
F:125-191
1b
CDC48_2-1s3sF02
F:125-191
1c
CDC48_2-1s3sF03
F:125-191
1d
CDC48_2-1s3sF04
F:125-191
1e
CDC48_2-1s3sF05
F:125-191
1f
CDC48_2-1s3sF06
F:125-191
Clan
:
P-loop_NTPase
(1112)
Family
:
AAA
(26)
Mus musculus (Mouse)
(5)
2a
AAA-1s3sF07
F:241-371
2b
AAA-1s3sF08
F:241-371
2c
AAA-1s3sF09
F:241-371
2d
AAA-1s3sF10
F:241-371
2e
AAA-1s3sF11
F:241-371
2f
AAA-1s3sF12
F:241-371
Clan
:
Ubiquitin
(279)
Family
:
UBX
(7)
Rattus norvegicus (Rat)
(2)
3a
UBX-1s3sI01
I:314-326
3b
UBX-1s3sI02
I:314-326
3c
UBX-1s3sI03
I:314-326
Clan
:
no clan defined [family: CDC48_N]
(7)
Family
:
CDC48_N
(7)
Mus musculus (Mouse)
(3)
4a
CDC48_N-1s3sF13
F:25-108
4b
CDC48_N-1s3sF14
F:25-108
4c
CDC48_N-1s3sF15
F:25-108
4d
CDC48_N-1s3sF16
F:25-108
4e
CDC48_N-1s3sF17
F:25-108
4f
CDC48_N-1s3sF18
F:25-108
[
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