SMTL ID : 4n2a.1

Crystal structure of Protein Arginine Deiminase 2 (5 mM Ca2+)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

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

MPD.1: 8 residues within 4Å: Chain A: Y.237, E.239, H.258, V.259, V.260, K.261, L.269, F.271 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.237, A:Y.237, A:K.261, A:L.269 MPD.2: 8 residues within 4Å: Chain A: S.454, S.455, F.456, P.457, E.482, L.483, Y.484, W.571 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:E.482, A:Y.484, A:W.571, A:W.571 Hydrogen bonds: A:S.455 Water bridges: A:E.482, A:E.482, A:E.482 MPD.3: 4 residues within 4Å: 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.10: 6 residues within 4Å: Chain A: I.547, K.551, I.552, N.555, L.558, F.605 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.547, A:K.551, A:L.558, A:F.605, A:F.605 Hydrogen bonds: A:N.555 MPD.12: 8 residues within 4Å: Chain B: Y.237, E.239, H.258, V.259, V.260, K.261, L.269, F.271 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.237, B:Y.237, B:K.261, B:L.269 MPD.13: 8 residues within 4Å: Chain B: S.454, S.455, F.456, P.457, E.482, L.483, Y.484, W.571 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:E.482, B:Y.484, B:W.571, B:W.571 Hydrogen bonds: B:S.455 Water bridges: B:E.482, B:E.482, B:E.482, B:E.482 MPD.14: 4 residues within 4Å: Chain A: E.220, Y.257, V.259, L.303 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.257, A:V.259, A:L.303 MPD.21: 6 residues within 4Å: Chain B: I.547, K.551, I.552, N.555, L.558, F.605 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.547, B:K.551, B:L.558, B:F.605, B:F.605 Hydrogen bonds: B:N.555

10 x CA: CALCIUM ION(Non-covalent)

CA.4: 3 residues within 4Å: Chain A: D.187, D.190, K.192 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.187, A:K.192, H2O.3, H2O.4, H2O.5 CA.5: 7 residues within 4Å: Chain A: N.175, D.177, E.179, D.187, D.198, D.201 Ligands: CA.6 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.177, A:E.179, A:D.187, A:D.198, A:D.201 CA.6: 6 residues within 4Å: Chain A: D.177, E.179, D.201, K.384, D.410 Ligands: CA.5 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.177, A:E.179, A:D.410, H2O.3, H2O.4 CA.8: 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.4 CA.9: 5 residues within 4Å: Chain A: Q.371, 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.1, H2O.3 CA.15: 3 residues within 4Å: Chain B: D.187, D.190, K.192 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.187, B:K.192, H2O.24, H2O.25, H2O.26 CA.16: 7 residues within 4Å: Chain B: N.175, D.177, E.179, D.187, D.198, D.201 Ligands: CA.17 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.177, B:E.179, B:D.187, B:D.198, B:D.201 CA.17: 6 residues within 4Å: Chain B: D.177, E.179, D.201, K.384, D.410 Ligands: CA.16 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.177, B:E.179, B:D.410, H2O.24, H2O.25 CA.19: 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.25 CA.20: 5 residues within 4Å: Chain B: Q.371, 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.22, H2O.24

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

ACT.7: 3 residues within 4Å: Chain A: N.611, I.613, T.670 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.670 ACT.11: 2 residues within 4Å: Chain A: R.463, R.469 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.469 Water bridges: A:R.469 ACT.18: 3 residues within 4Å: Chain B: N.611, I.613, T.670 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.670 ACT.22: 2 residues within 4Å: Chain B: R.463, R.469 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:R.469 Water bridges: B:R.469

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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