SMTL ID : 4n25.1

Crystal structure of Protein Arginine Deiminase 2 (250 uM Ca2+)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

homo-dimer

Ligands

2 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.1: 6 residues within 4Å: Chain A: S.455, P.457, E.482, L.483, W.571, I.575 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.457, A:I.575 Water bridges: A:E.482, A:E.482, A:E.482 MRD.10: 6 residues within 4Å: Chain B: S.455, P.457, E.482, L.483, W.571, I.575 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:P.457, B:I.575 Water bridges: B:E.482, B:E.482, B:E.482, B:E.482

4 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.2: 5 residues within 4Å: Chain A: L.458 Chain B: E.220, Y.257, V.259, L.303 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.257, B:V.259, B:L.303 MPD.9: 9 residues within 4Å: Chain A: F.341, Q.371, N.611, M.612, I.613, P.622, D.655, G.669, T.670 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.613, A:P.622, A:T.670 Hydrogen bonds: A:D.655, A:T.670 MPD.11: 5 residues within 4Å: Chain A: E.220, Y.257, V.259, L.303 Chain B: L.458 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.257, A:V.259, A:L.303 MPD.18: 9 residues within 4Å: Chain B: F.341, Q.371, N.611, M.612, I.613, P.622, D.655, G.669, T.670 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.613, B:P.622, B:T.670 Hydrogen bonds: B:D.655, B:D.655, B:T.670

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 5 residues within 4Å: Chain A: G.529, H.530, E.532, A.533, Q.628 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:E.532 Hydrogen bonds: A:Q.628 Water bridges: A:H.530, A:E.532 Salt bridges: A:H.530 ACT.12: 5 residues within 4Å: Chain B: G.529, H.530, E.532, A.533, Q.628 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:E.532 Hydrogen bonds: B:Q.628 Water bridges: B:E.532 Salt bridges: B:H.530

10 x CA: CALCIUM ION(Non-covalent)

CA.4: 5 residues within 4Å: Chain A: D.144, D.146, D.148, V.150, E.152 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.144, A:D.146, A:D.148, A:V.150, A:E.152, H2O.14 CA.5: 6 residues within 4Å: Chain A: N.175, D.177, D.187, D.198, D.201 Ligands: CA.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.187, A:D.198, A:D.201 CA.6: 4 residues within 4Å: Chain A: D.177, D.201, D.410 Ligands: CA.5 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.201, A:D.201, A:D.410, H2O.6, H2O.14 CA.7: 3 residues within 4Å: Chain A: D.187, D.190, K.192 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.187, A:D.190, A:K.192, H2O.13, H2O.15 CA.8: 4 residues within 4Å: Chain A: E.375, F.429, L.432, E.433 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.375, A:F.429, A:L.432, H2O.4, H2O.15 CA.13: 5 residues within 4Å: Chain B: D.144, D.146, D.148, V.150, E.152 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.144, B:D.146, B:D.148, B:V.150, B:E.152, H2O.34 CA.14: 6 residues within 4Å: Chain B: N.175, D.177, D.187, D.198, D.201 Ligands: CA.15 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.187, B:D.198, B:D.201 CA.15: 4 residues within 4Å: Chain B: D.177, D.201, D.410 Ligands: CA.14 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.201, B:D.201, B:D.410, H2O.26, H2O.34 CA.16: 3 residues within 4Å: Chain B: D.187, D.190, K.192 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.187, B:D.190, B:K.192, H2O.33, H2O.35 CA.17: 4 residues within 4Å: Chain B: E.375, F.429, L.432, E.433 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.375, B:F.429, B:L.432, H2O.24, H2O.34

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Slade, D.J. et al., Protein arginine deiminase 2 binds calcium in an ordered fashion: implications for inhibitor design. Acs Chem.Biol. (2015)

Release Date

2015-02-04

Peptides

Protein-arginine deiminase type-2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Protein-arginine deiminase type-2

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