SMTL ID : 4n2i.1

Crystal structure of Protein Arginine Deiminase 2 (D177A, 10 mM Ca2+)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

MPD.1: 7 residues within 4Å: Chain A: Y.237, H.258, V.259, V.260, K.261, L.269, F.271 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: 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 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:P.457, 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, A:E.482, A:E.482 MPD.3: 5 residues within 4Å: Chain A: L.458 Chain B: E.220, Y.257, V.259, L.303 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.259, B:L.303 MPD.10: 10 residues within 4Å: Chain A: F.341, R.368, N.611, I.613, G.620, P.622, I.653, D.655, G.669, T.670 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.341, A:I.613, A:I.653 Hydrogen bonds: A:N.611 MPD.12: 7 residues within 4Å: Chain B: Y.237, H.258, V.259, V.260, K.261, L.269, F.271 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: 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 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:P.457, 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, B:E.482, B:E.482 MPD.14: 5 residues within 4Å: Chain A: E.220, Y.257, V.259, L.303 Chain B: L.458 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.259, A:L.303 MPD.21: 10 residues within 4Å: Chain B: F.341, R.368, N.611, I.613, G.620, P.622, I.653, D.655, G.669, T.670 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.341, B:I.613, B:I.653 Hydrogen bonds: B:N.611

10 x CA: CALCIUM ION(Non-covalent)

CA.4: 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.2, H2O.18 CA.5: 6 residues within 4Å: Chain A: N.175, D.177, E.179, D.187, D.201 Ligands: CA.6 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.177, A:E.179, A:D.187, A:D.201, H2O.7 CA.6: 5 residues within 4Å: Chain A: D.177, E.179, D.201, D.410 Ligands: CA.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.177, A:E.179, A:D.201, A:D.201, H2O.17 CA.7: 3 residues within 4Å: Chain A: D.187, D.190, K.192 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.187, A:D.190, A:K.192, H2O.10 CA.11: 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.18 CA.15: 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.20, H2O.35 CA.16: 6 residues within 4Å: Chain B: N.175, D.177, E.179, D.187, D.201 Ligands: CA.17 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.177, B:E.179, B:D.187, B:D.201, H2O.25 CA.17: 5 residues within 4Å: Chain B: D.177, E.179, D.201, D.410 Ligands: CA.16 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.177, B:E.179, B:D.201, B:D.201, H2O.35 CA.18: 3 residues within 4Å: Chain B: D.187, D.190, K.192 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.187, B:D.190, B:K.192, H2O.28 CA.22: 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.35

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

ACT.8: 3 residues within 4Å: Chain A: R.463, R.469, E.482 No protein-ligand interaction detected (PLIP) ACT.9: 3 residues within 4Å: Chain A: N.117, Y.119, P.126 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.126 Hydrogen bonds: A:S.62, A:N.117 Water bridges: A:N.85 Salt bridges: A:K.87 ACT.19: 3 residues within 4Å: Chain B: R.463, R.469, E.482 No protein-ligand interaction detected (PLIP) ACT.20: 3 residues within 4Å: Chain B: N.117, Y.119, P.126 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:P.126 Hydrogen bonds: B:S.62, B:N.117, B:Y.119 Water bridges: B:N.85 Salt bridges: B:K.87

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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