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Asym. Unit
Info
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
[
close entry info
]
Hetero Components
(3, 9)
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
1
Ligand/Ion
N-[(E)-2-AMINO-1-(3-{[AMINO(IMINO)METHYL]AMINO}PROPYL)-2-HYDROXYVINYL]BENZAMIDE
2
CA
5
Ligand/Ion
CALCIUM ION
3
SO4
3
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
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
[
close Site info
]
SAPs(SNPs)/Variants
(9, 9)
Info
(mutated residues are not available)
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)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
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]
Exons
(16, 16)
Info
All Exons
Exon 1.1b (A:4-31)
Exon 1.2 (A:31-91 (gaps))
Exon 1.3 (A:92-114)
Exon 1.6 (A:114-136 (gaps))
Exon 1.7 (A:137-176)
Exon 1.8 (A:176-217)
Exon 1.9 (A:225-277)
Exon 1.10 (A:278-312)
Exon 1.11a (A:312-349)
Exon 1.12b (A:350-385)
Exon 1.14 (A:386-437)
Exon 1.15 (A:437-485)
Exon 1.16b (A:486-520)
Exon 1.17b (A:520-543)
Exon 1.18 (A:544-586)
Exon 1.19 (A:587-663)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1b
02: Boundary 1.1b/1.2
03: Boundary 1.2/1.3
04: Boundary 1.3/1.6
05: Boundary 1.6/1.7
06: Boundary 1.7/1.8
07: Boundary 1.8/1.9
08: Boundary 1.9/1.10
09: Boundary 1.10/1.11a
10: Boundary 1.11a/1.12b
11: Boundary 1.12b/1.14
12: Boundary 1.14/1.15
13: Boundary 1.15/1.16b
14: Boundary 1.16b/1.17b
15: Boundary 1.17b/1.18
16: Boundary 1.18/1.19
17: Boundary 1.19/-
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
1.1b
ENST00000375448
1b
ENSE00001883200
chr1:
17634692-17634809
118
PADI4_HUMAN
1-31
31
1
A:4-31
28
1.2
ENST00000375448
2
ENSE00001268578
chr1:
17657464-17657644
181
PADI4_HUMAN
31-91
61
1
A:31-91 (gaps)
61
1.3
ENST00000375448
3
ENSE00001044965
chr1:
17660438-17660504
67
PADI4_HUMAN
92-114
23
1
A:92-114
23
1.6
ENST00000375448
6
ENSE00001044983
chr1:
17662654-17662721
68
PADI4_HUMAN
114-136
23
1
A:114-136 (gaps)
23
1.7
ENST00000375448
7
ENSE00001044981
chr1:
17664533-17664650
118
PADI4_HUMAN
137-176
40
1
A:137-176
40
1.8
ENST00000375448
8
ENSE00001044989
chr1:
17666183-17666308
126
PADI4_HUMAN
176-218
43
1
A:176-217
42
1.9
ENST00000375448
9
ENSE00001268541
chr1:
17668438-17668616
179
PADI4_HUMAN
218-277
60
1
A:225-277
53
1.10
ENST00000375448
10
ENSE00001044974
chr1:
17668794-17668897
104
PADI4_HUMAN
278-312
35
1
A:278-312
35
1.11a
ENST00000375448
11a
ENSE00001044969
chr1:
17672523-17672634
112
PADI4_HUMAN
312-349
38
1
A:312-349
38
1.12b
ENST00000375448
12b
ENSE00001044980
chr1:
17674436-17674543
108
PADI4_HUMAN
350-385
36
1
A:350-385
36
1.14
ENST00000375448
14
ENSE00001044967
chr1:
17681028-17681182
155
PADI4_HUMAN
386-437
52
1
A:386-437
52
1.15
ENST00000375448
15
ENSE00001044986
chr1:
17682478-17682622
145
PADI4_HUMAN
437-485
49
1
A:437-485
49
1.16b
ENST00000375448
16b
ENSE00001044971
chr1:
17682852-17682954
103
PADI4_HUMAN
486-520
35
1
A:486-520
35
1.17b
ENST00000375448
17b
ENSE00001044973
chr1:
17685333-17685403
71
PADI4_HUMAN
520-543
24
1
A:520-543
24
1.18
ENST00000375448
18
ENSE00001044963
chr1:
17685775-17685903
129
PADI4_HUMAN
544-586
43
1
A:544-586
43
1.19
ENST00000375448
19
ENSE00001467124
chr1:
17690017-17690499
483
PADI4_HUMAN
587-663
77
1
A:587-663
77
[
close EXON info
]
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
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
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)
View:
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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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]
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Chain A
Asymmetric Unit 1
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