SMTL ID : 4n2g.1

Crystal structure of Protein Arginine Deiminase 2 (D169A, 10 mM Ca2+)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

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

MPD.1: 8 residues within 4Å: Chain A: Y.237, E.239, I.248, H.258, V.260, K.261, L.269, F.271 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.237, A:Y.237, A:I.248, A:K.261, A:L.269 Hydrogen bonds: 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 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.456, 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.7: 5 residues within 4Å: Chain A: K.545, A.604, F.605, F.662, L.663 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.545, A:F.662 MPD.9: 9 residues within 4Å: Chain A: F.341, Q.371, N.611, M.612, I.613, G.620, P.622, G.669, T.670 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.341, A:I.613, A:T.670 Hydrogen bonds: A:Q.371, A:N.611, A:G.620 MPD.11: 3 residues within 4Å: Chain A: E.220, Y.257 Chain B: L.458 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.257, B:L.458 MPD.12: 8 residues within 4Å: Chain B: Y.237, E.239, I.248, H.258, V.260, K.261, L.269, F.271 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.237, B:Y.237, B:I.248, B:K.261, B:L.269 Hydrogen bonds: B:H.258 MPD.13: 8 residues within 4Å: Chain B: S.454, S.455, F.456, P.457, E.482, L.483, Y.484, W.571 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.456, 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.18: 5 residues within 4Å: Chain B: K.545, A.604, F.605, F.662, L.663 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:K.545, B:F.662 MPD.20: 9 residues within 4Å: Chain B: F.341, Q.371, N.611, M.612, I.613, G.620, P.622, G.669, T.670 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.341, B:I.613, B:T.670 Hydrogen bonds: B:Q.371, B:N.611, B:G.620 MPD.22: 3 residues within 4Å: Chain A: L.458 Chain B: E.220, Y.257 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.257, A:L.458

8 x CA: CALCIUM ION(Non-covalent)

CA.3: 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:F.429, A:L.432, A:E.433, H2O.11, H2O.11 CA.4: 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.4, H2O.11 CA.5: 7 residues within 4Å: Chain A: N.175, D.177, E.179, D.187, D.198, D.201 Ligands: CA.4 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: 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.14: 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:F.429, B:L.432, B:E.433, H2O.28, H2O.28 CA.15: 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.20, H2O.27 CA.16: 7 residues within 4Å: Chain B: N.175, D.177, E.179, D.187, D.198, D.201 Ligands: CA.15 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: 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.30

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

ACT.8: 5 residues within 4Å: Chain A: L.276, C.277, F.278, V.414, R.416 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.278 Hydrogen bonds: A:L.276 Water bridges: A:R.416, A:R.416 Salt bridges: A:R.416 ACT.19: 5 residues within 4Å: Chain B: L.276, C.277, F.278, V.414, R.416 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.278 Hydrogen bonds: B:L.276 Water bridges: B:R.416, B:R.416 Salt bridges: B:R.416

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 7 residues within 4Å: Chain A: N.323, D.494, M.497, S.498, V.610, N.611, M.612 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.323, A:D.494, A:M.612, A:M.612 Water bridges: A:F.499 GOL.21: 7 residues within 4Å: Chain B: N.323, D.494, M.497, S.498, V.610, N.611, M.612 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.323, B:D.494, B:M.612, B:M.612 Water bridges: B:F.499

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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