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5AK7
Asym. Unit
Info
Asym.Unit (165 KB)
Biol.Unit 1 (158 KB)
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(1)
Title
:
STRUCTURE OF WT PORPHYROMONAS GINGIVALIS PEPTIDYLARGININE DEIMINASE
Authors
:
J. Kopec, A. Montgomery, L. Shrestha, W. Kiyani, R. Nowak, N. Burgess-B P. J. Venables, W. W. Yue
Date
:
02 Mar 15 (Deposition) - 22 Jul 15 (Release) - 25 May 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.46
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Hydrolase, Ppad
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. B. Montgomery, J. Kopec, L. Shrestha, M. L. Thezenas, N. A. Burgess-Brown, R. Fischer, W. W. Yue, P. J. Venables
Crystal Structure Of Porphyromonas Gingivalis Peptidylarginine Deiminase: Implications For Autoimmunity In Rheumatoid Arthritis.
Ann. Rheum. Dis. V. 75 1255 2016
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Hetero Components
(4, 20)
Info
All Hetero Components
1a: ALANINE (ALAa)
2a: ARGININE (ARGa)
3a: 1,2-ETHANEDIOL (EDOa)
3b: 1,2-ETHANEDIOL (EDOb)
3c: 1,2-ETHANEDIOL (EDOc)
3d: 1,2-ETHANEDIOL (EDOd)
3e: 1,2-ETHANEDIOL (EDOe)
3f: 1,2-ETHANEDIOL (EDOf)
3g: 1,2-ETHANEDIOL (EDOg)
3h: 1,2-ETHANEDIOL (EDOh)
3i: 1,2-ETHANEDIOL (EDOi)
3j: 1,2-ETHANEDIOL (EDOj)
3k: 1,2-ETHANEDIOL (EDOk)
3l: 1,2-ETHANEDIOL (EDOl)
3m: 1,2-ETHANEDIOL (EDOm)
3n: 1,2-ETHANEDIOL (EDOn)
3o: 1,2-ETHANEDIOL (EDOo)
3p: 1,2-ETHANEDIOL (EDOp)
3q: 1,2-ETHANEDIOL (EDOq)
4a: SODIUM ION (NAa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ALA
1
Mod. Amino Acid
ALANINE
2
ARG
1
Mod. Amino Acid
ARGININE
3
EDO
17
Ligand/Ion
1,2-ETHANEDIOL
4
NA
1
Ligand/Ion
SODIUM ION
[
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Sites
(20, 20)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER A:125 , TYR A:126 , TRP A:127 , EDO A:1480
BINDING SITE FOR RESIDUE EDO A1466
02
AC2
SOFTWARE
TYR A:61 , GLU A:62 , PRO A:246 , TYR A:361 , TYR A:449 , HOH A:2029 , HOH A:2375
BINDING SITE FOR RESIDUE EDO A1467
03
AC3
SOFTWARE
LYS A:248 , GLU A:283 , TYR A:285 , ASP A:456 , HOH A:2308
BINDING SITE FOR RESIDUE EDO A1468
04
AC4
SOFTWARE
ASN A:247 , PRO A:450 , ASP A:456 , PRO A:457 , HOH A:2267 , HOH A:2269 , HOH A:2308
BINDING SITE FOR RESIDUE EDO A1469
05
AC5
SOFTWARE
LYS A:365 , TYR A:367 , GLU A:381 , ASP A:383 , HIS A:419 , HOH A:2379 , HOH A:2397 , HOH A:2478
BINDING SITE FOR RESIDUE EDO A1470
06
AC6
SOFTWARE
ASN A:202 , LEU A:205 , HOH A:2214
BINDING SITE FOR RESIDUE EDO A1471
07
AC7
SOFTWARE
TYR A:399 , TYR A:422 , PHE A:424 , THR A:425
BINDING SITE FOR RESIDUE EDO A1472
08
AC8
SOFTWARE
PRO A:54 , THR A:140 , HOH A:2479
BINDING SITE FOR RESIDUE EDO A1473
09
AC9
SOFTWARE
PRO A:328 , PRO A:455 , LYS A:459 , HOH A:2453 , HOH A:2473
BINDING SITE FOR RESIDUE EDO A1474
10
BC1
SOFTWARE
LYS A:213
BINDING SITE FOR RESIDUE EDO A1475
11
BC2
SOFTWARE
TYR A:270 , HOH A:2244 , HOH A:2289 , HOH A:2480
BINDING SITE FOR RESIDUE EDO A1476
12
BC3
SOFTWARE
SER A:114 , SER A:191 , GLN A:274 , THR A:275 , CYS A:276 , ALA A:277 , TYR A:282 , HOH A:2096 , HOH A:2196
BINDING SITE FOR RESIDUE EDO A1477
13
BC4
SOFTWARE
ASP A:117 , PHE A:118 , TYR A:167 , LYS A:281 , HOH A:2099
BINDING SITE FOR RESIDUE EDO A1478
14
BC5
SOFTWARE
ASN A:211 , THR A:221 , HIS A:222 , HIS A:223 , HOH A:2229
BINDING SITE FOR RESIDUE EDO A1479
15
BC6
SOFTWARE
ARG A:70 , TYR A:126 , EDO A:1466 , HOH A:2048
BINDING SITE FOR RESIDUE EDO A1480
16
BC7
SOFTWARE
VAL A:284 , TYR A:285 , HOH A:2306
BINDING SITE FOR RESIDUE EDO A1481
17
BC8
SOFTWARE
SER A:203 , SER A:204 , SER A:206
BINDING SITE FOR RESIDUE EDO A1482
18
BC9
SOFTWARE
ASP A:147 , PHE A:148 , ASP A:158 , HOH A:2123 , HOH A:2143
BINDING SITE FOR RESIDUE NA A1483
19
CC1
SOFTWARE
TRP A:127 , ARG A:154 , TYR A:233 , ARG A:1002
BINDING SITE FOR RESIDUE ALA A1001
20
CC2
SOFTWARE
TRP A:127 , ASP A:130 , ARG A:152 , ARG A:154 , GLY A:182 , TYR A:233 , ILE A:234 , HIS A:236 , ASP A:238 , THR A:346 , CYS A:351 , ALA A:1001 , HOH A:2122 , HOH A:2259 , HOH A:2368
BINDING SITE FOR RESIDUE ARG A1002
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
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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.
SCOP Domains
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CATH Domains
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Pfam Domains
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Chain A
Asymmetric Unit 1
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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Asym.Unit (165 KB)
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