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4YTG
Asym. Unit
Info
Asym.Unit (154 KB)
Biol.Unit 1 (149 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF PORPHYROMONAS GINGIVALIS PEPTIDYLARGININE DEIMINASE (PPAD) MUTANT C351A IN COMPLEX WITH DIPEPTIDE MET-ARG.
Authors
:
T. Goulas, D. Mizgalska, I. Garcia-Ferrer, T. Kantyka, T. Guevara, B. Szmigielski, A. Sroka, C. Millan, I. Uson, F. Veillard, B. Potempa, M. Sola, J. Potempa, F. X. Gomis-Ruth
Date
:
17 Mar 15 (Deposition) - 01 Jul 15 (Release) - 28 Sep 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Peptidylarginine Deiminase, Citrullination, Hydrolase
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Goulas, D. Mizgalska, I. Garcia-Ferrer, T. Kantyka, T. Guevara, B. Szmigielski, A. Sroka, C. Millan, I. Uson, F. Veillard, B. Potempa, P. Mydel, M. Sola, J. Potempa, F. X. Gomis-Ruth
Structure And Mechanism Of A Bacterial Host-Protein Citrullinating Virulence Factor, Porphyromonas Gingivalis Peptidylarginine Deiminase.
Sci Rep V. 5 11969 2015
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Hetero Components
(7, 12)
Info
All Hetero Components
1a: ARGININE (ARGa)
2a: AZIDE ION (AZIa)
2b: AZIDE ION (AZIb)
3a: CHLORIDE ION (CLa)
4a: CYSTEINE (CYSa)
5a: GLYCEROL (GOLa)
5b: GLYCEROL (GOLb)
5c: GLYCEROL (GOLc)
5d: GLYCEROL (GOLd)
5e: GLYCEROL (GOLe)
6a: METHIONINE (METa)
7a: SODIUM ION (NAa)
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Label:
No.
Name
Count
Type
Full Name
1
ARG
1
Mod. Amino Acid
ARGININE
2
AZI
2
Ligand/Ion
AZIDE ION
3
CL
1
Ligand/Ion
CHLORIDE ION
4
CYS
1
Mod. Amino Acid
CYSTEINE
5
GOL
5
Ligand/Ion
GLYCEROL
6
MET
1
Mod. Amino Acid
METHIONINE
7
NA
1
Ligand/Ion
SODIUM ION
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Sites
(12, 12)
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: AD1 (SOFTWARE)
11: AD2 (SOFTWARE)
12: AD3 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:147 , PHE A:148 , ASP A:158 , HOH A:797
binding site for residue NA A 501
02
AC2
SOFTWARE
TYR A:378 , PHE A:424 , THR A:425 , GLY A:426 , LEU A:427 , PHE A:460 , CYS A:462
binding site for residue CYS A 502
03
AC3
SOFTWARE
TRP A:127 , ARG A:154 , TYR A:233 , ARG A:504 , HOH A:724
binding site for residue MET A 503
04
AC4
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 , ALA A:351 , MET A:503 , HOH A:764 , HOH A:914
binding site for residue ARG A 504
05
AC5
SOFTWARE
ILE A:149 , LYS A:176 , ASN A:202 , SER A:204 , HOH A:798 , HOH A:804 , HOH A:824
binding site for residue GOL A 505
06
AC6
SOFTWARE
ASP A:266 , TYR A:270 , HOH A:631 , HOH A:740 , HOH A:1001
binding site for residue GOL A 506
07
AC7
SOFTWARE
VAL A:55 , ARG A:56 , GLY A:219 , LYS A:365 , TYR A:367 , HOH A:643 , HOH A:771 , HOH A:904
binding site for residue GOL A 507
08
AC8
SOFTWARE
ASN A:247 , LYS A:248 , GLU A:283 , PRO A:450 , ASP A:456 , AZI A:512 , HOH A:815 , HOH A:869
binding site for residue GOL A 508
09
AC9
SOFTWARE
TYR A:399 , TYR A:422 , SER A:423 , PHE A:424 , THR A:425 , LEU A:427 , HOH A:674
binding site for residue GOL A 509
10
AD1
SOFTWARE
ASN A:49
binding site for residue CL A 510
11
AD2
SOFTWARE
GLU A:232 , ASN A:235 , HOH A:604 , HOH A:678
binding site for residue AZI A 511
12
AD3
SOFTWARE
LYS A:248 , GLU A:283 , TYR A:285 , ASP A:456 , GOL A:508
binding site for residue AZI A 512
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are not available)
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PROSITE Patterns/Profiles
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Exons
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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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Asym.Unit (154 KB)
Header - Asym.Unit
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