SMTL ID : 4n2l.1

Crystal structure of Protein Arginine Deiminase 2 (Q350A, 10 mM Ca2+)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

MPD.1: 7 residues within 4Å: Chain A: Y.237, E.239, H.258, V.259, V.260, K.261, F.271 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.237, A:Y.237, A:K.261 Water bridges: A:H.258, A:H.258 MPD.2: 8 residues within 4Å: Chain A: S.454, S.455, F.456, P.457, E.482, L.483, Y.484, W.571 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.456, A:E.482, A:Y.484 Hydrogen bonds: A:S.455 MPD.3: 5 residues within 4Å: Chain B: E.220, Y.257, V.259, L.294, L.303 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.257, B:V.259, B:L.303 Hydrogen bonds: B:E.220 MPD.14: 6 residues within 4Å: Chain A: I.547, A.604, F.605, F.662, L.663, G.664 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.547, A:F.605 MPD.15: 10 residues within 4Å: Chain A: F.341, N.611, I.613, G.620, I.621, P.622, I.653, D.655, C.668, T.670 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.613, A:I.653, A:T.670 Hydrogen bonds: A:D.655, A:T.670 Water bridges: A:T.670 MPD.16: 7 residues within 4Å: Chain B: Y.237, E.239, H.258, V.259, V.260, K.261, F.271 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.237, B:Y.237, B:K.261 Water bridges: B:H.258, B:V.259 MPD.17: 8 residues within 4Å: Chain B: S.454, S.455, F.456, P.457, E.482, L.483, Y.484, W.571 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.456, B:E.482, B:Y.484 Hydrogen bonds: B:S.455 MPD.18: 5 residues within 4Å: Chain A: E.220, Y.257, V.259, L.294, L.303 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.257, A:V.259, A:L.303 Hydrogen bonds: A:E.220 MPD.29: 6 residues within 4Å: Chain B: I.547, A.604, F.605, F.662, L.663, G.664 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.547, B:F.605 MPD.30: 10 residues within 4Å: Chain B: F.341, N.611, I.613, G.620, I.621, P.622, I.653, D.655, C.668, T.670 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.613, B:I.653, B:T.670 Hydrogen bonds: B:T.670 Water bridges: B:T.670

10 x CA: CALCIUM ION(Non-covalent)

CA.4: 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.2, H2O.15 CA.5: 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.8, H2O.10 CA.6: 7 residues within 4Å: Chain A: N.175, D.177, E.179, D.187, D.198, D.201 Ligands: CA.7 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.7: 6 residues within 4Å: Chain A: D.177, E.179, D.201, K.384, D.410 Ligands: CA.6 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.177, A:E.179, A:D.410, H2O.4, 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.10 CA.19: 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.18, H2O.32 CA.20: 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.19, H2O.24, H2O.26 CA.21: 7 residues within 4Å: Chain B: N.175, D.177, E.179, D.187, D.198, D.201 Ligands: CA.22 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.22: 6 residues within 4Å: Chain B: D.177, E.179, D.201, K.384, D.410 Ligands: CA.21 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.177, B:E.179, B:D.410, H2O.20, H2O.20 CA.23: 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.26

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

ACT.9: 4 residues within 4Å: Chain A: R.463, R.469, K.473, E.482 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.469 Water bridges: A:R.469 ACT.10: 7 residues within 4Å: Chain A: V.174, R.189, L.276, C.277, F.278, V.414, R.416 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.174, A:F.278 Hydrogen bonds: A:R.189, A:F.278 Water bridges: A:E.186, A:T.415 Salt bridges: A:R.416 ACT.11: 2 residues within 4Å: Chain A: S.160, W.161 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.161, A:W.161 ACT.12: 6 residues within 4Å: Chain A: D.144, G.149, M.202, S.203, Q.204, H.383 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:D.144 Hydrogen bonds: A:G.149, A:Q.204 Water bridges: A:Q.204 Salt bridges: A:H.383 ACT.13: 3 residues within 4Å: Chain A: A.109, S.110, S.111 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.109 ACT.24: 4 residues within 4Å: Chain B: R.463, R.469, K.473, E.482 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.469 Water bridges: B:R.469, B:E.482 ACT.25: 7 residues within 4Å: Chain B: V.174, R.189, L.276, C.277, F.278, V.414, R.416 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:V.174, B:F.278 Hydrogen bonds: B:R.189, B:F.278 Water bridges: B:E.186, B:T.415 Salt bridges: B:R.416 ACT.26: 2 residues within 4Å: Chain B: S.160, W.161 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.161, B:W.161 ACT.27: 6 residues within 4Å: Chain B: D.144, G.149, M.202, S.203, Q.204, H.383 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:D.144 Hydrogen bonds: B:G.149, B:Q.204 Water bridges: B:Q.204 Salt bridges: B:H.383 ACT.28: 3 residues within 4Å: Chain B: A.109, S.110, S.111 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.109

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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