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1WDA
Biol. Unit 1
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Asym.Unit (112 KB)
Biol.Unit 1 (206 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN PEPTIDYLARGININE DEIMINASE TYPE4 (PAD4) IN COMPLEX WITH BENZOYL-L-ARGININE AMIDE
Authors
:
K. Arita, H. Hashimoto, T. Shimizu, K. Nakashima, M. Yamada, M. Sato
Date
:
12 May 04 (Deposition) - 13 Jul 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Keywords
:
Post-Translational Enzyme, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Arita, H. Hashimoto, T. Shimizu, K. Nakashima, M. Yamada, M. Sato
Structural Basis For Ca(2+)-Induced Activation Of Human Pad
Nat. Struct. Mol. Biol. V. 11 777 2004
[
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Hetero Components
(2, 8)
Info
All Hetero Components
1a: N-[(E)-2-AMINO-1-(3-{[AMINO(IMINO)... (BAGa)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
2e: CALCIUM ION (CAe)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BAG
2
Ligand/Ion
N-[(E)-2-AMINO-1-(3-{[AMINO(IMINO)METHYL]AMINO}PROPYL)-2-HYDROXYVINYL]BENZAMIDE
2
CA
-1
Ligand/Ion
CALCIUM ION
3
SO4
6
Ligand/Ion
SULFATE ION
[
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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
GLN A:349 , GLU A:353 , PHE A:407 , LEU A:410 , GLU A:411 , HOH A:919 , HOH A:942
BINDING SITE FOR RESIDUE CA A 900
2
AC2
SOFTWARE
ASN A:153 , ASP A:155 , ASP A:157 , ASP A:165 , ASP A:176 , ASP A:179
BINDING SITE FOR RESIDUE CA A 901
3
AC3
SOFTWARE
ASP A:155 , ASP A:157 , ASP A:179 , ASP A:388
BINDING SITE FOR RESIDUE CA A 902
4
AC4
SOFTWARE
GLU A:351 , ASP A:369 , SER A:370 , ASN A:373 , HOH A:1065
BINDING SITE FOR RESIDUE CA A 903
5
AC5
SOFTWARE
ASP A:165 , ASP A:168 , GLU A:170 , HOH A:1059 , HOH A:1066
BINDING SITE FOR RESIDUE CA A 904
6
AC6
SOFTWARE
SER A:402 , GLY A:403 , ARG A:441
BINDING SITE FOR RESIDUE SO4 A 905
7
AC7
SOFTWARE
ARG A:495 , SER A:496 , LYS A:499 , LYS A:615
BINDING SITE FOR RESIDUE SO4 A 906
8
AC8
SOFTWARE
LYS A:525 , ASN A:528
BINDING SITE FOR RESIDUE SO4 A 907
9
AC9
SOFTWARE
TRP A:347 , GLN A:349 , ASP A:350 , ARG A:374 , GLY A:408 , HIS A:471 , ASP A:473 , ASN A:588 , ARG A:639 , HIS A:640 , ALA A:645 , HOH A:941
BINDING SITE FOR RESIDUE BAG A 801
[
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SAPs(SNPs)/Variants
(9, 18)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_053560 (R8H, chain A, )
2: VAR_053561 (T79M, chain A, )
3: VAR_020640 (A82A, chain A, )
4: VAR_027401 (D89N, chain A, )
5: VAR_027402 (P102T, chain A, )
6: VAR_020641 (A112A, chain A, )
7: VAR_027404 (M164T, chain A, )
8: VAR_053562 (D260N, chain A, )
9: VAR_020642 (S275F, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_053560
R
8
H
PADI4_HUMAN
Polymorphism
35381732
A
R
8
H
2
UniProt
VAR_053561
T
79
M
PADI4_HUMAN
Polymorphism
35809521
A
T
79
M
3
UniProt
VAR_020640
V
82
A
PADI4_HUMAN
Polymorphism
11203367
A
A
82
A
4
UniProt
VAR_027401
D
89
N
PADI4_HUMAN
Polymorphism
---
A
D
89
N
5
UniProt
VAR_027402
P
102
T
PADI4_HUMAN
Polymorphism
34309058
A
P
102
T
6
UniProt
VAR_020641
G
112
A
PADI4_HUMAN
Polymorphism
874881
A
A
112
A
7
UniProt
VAR_027404
M
164
T
PADI4_HUMAN
Polymorphism
11588132
A
M
164
T
8
UniProt
VAR_053562
D
260
N
PADI4_HUMAN
Polymorphism
35903413
A
D
260
N
9
UniProt
VAR_020642
S
275
F
PADI4_HUMAN
Polymorphism
1748020
A
S
275
F
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
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End label:
Sorry, no Info available
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Exons
(0, 0)
Info
All Exons
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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, 3)
Info
All SCOP Domains
1a: SCOP_d1wdaa1 (A:113-293)
2a: SCOP_d1wdaa2 (A:4-112)
3a: SCOP_d1wdaa3 (A:294-663)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Common fold of diphtheria toxin/transcription factors/cytochrome f
(364)
Superfamily
:
Peptidylarginine deiminase Pad4, middle domain
(12)
Family
:
Peptidylarginine deiminase Pad4, middle domain
(12)
Protein domain
:
Peptidylarginine deiminase Pad4, middle domain
(12)
Human (Homo sapiens) [TaxId: 9606]
(12)
1a
d1wdaa1
A:113-293
Fold
:
Cupredoxin-like
(545)
Superfamily
:
Cupredoxins
(543)
Family
:
Peptidylarginine deiminase Pad4, N-terminal domain
(12)
Protein domain
:
Peptidylarginine deiminase Pad4, N-terminal domain
(12)
Human (Homo sapiens) [TaxId: 9606]
(12)
2a
d1wdaa2
A:4-112
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Pentein, beta/alpha-propeller
(68)
Superfamily
:
Pentein
(68)
Family
:
Peptidylarginine deiminase Pad4, catalytic C-terminal domain
(12)
Protein domain
:
Peptidylarginine deiminase Pad4, catalytic C-terminal domain
(12)
Human (Homo sapiens) [TaxId: 9606]
(12)
3a
d1wdaa3
A:294-663
[
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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
(3, 3)
Info
all PFAM domains
1a: PFAM_PAD_1wdaA01 (A:278-663)
2a: PFAM_PAD_M_1wdaA02 (A:113-273)
3a: PFAM_PAD_N_1wdaA03 (A:4-111)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
GME
(20)
Family
:
PAD
(3)
Homo sapiens (Human)
(3)
1a
PAD-1wdaA01
A:278-663
Clan
:
no clan defined [family: PAD_M]
(3)
Family
:
PAD_M
(3)
Homo sapiens (Human)
(3)
2a
PAD_M-1wdaA02
A:113-273
Clan
:
no clan defined [family: PAD_N]
(3)
Family
:
PAD_N
(3)
Homo sapiens (Human)
(3)
3a
PAD_N-1wdaA03
A:4-111
[
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]
Atom Selection
(currently selected atoms:
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)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Asymmetric Unit 1
Asymmetric Unit 2
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