SMTL ID : 4n2f.1

Crystal structure of Protein Arginine Deiminase 2 (D169A, 0 mM Ca2+)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

MPD.1: 5 residues within 4Å: Chain A: L.458 Chain B: E.220, Y.257, V.259, L.303 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.257, B:Y.257, B:V.259, A:L.458 Water bridges: A:L.458 MPD.2: 7 residues within 4Å: Chain A: D.280, L.390, V.414, R.416, V.467, V.468, F.471 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.390, A:R.416, A:V.467, A:V.468, A:F.471 MPD.5: 7 residues within 4Å: Chain A: S.455, F.456, P.457, E.482, L.483, Y.484, W.571 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.456, A:W.571 Hydrogen bonds: A:S.455 Water bridges: A:E.482, A:E.482, A:E.482 MPD.6: 10 residues within 4Å: Chain A: F.341, Q.371, N.611, M.612, I.613, G.620, P.622, D.655, G.669, T.670 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.341, A:I.613, A:P.622 Hydrogen bonds: A:T.670 MPD.8: 5 residues within 4Å: Chain A: E.220, Y.257, V.259, L.303 Chain B: L.458 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.257, A:Y.257, A:V.259, B:L.458 Water bridges: B:L.458 MPD.9: 7 residues within 4Å: Chain B: D.280, L.390, V.414, R.416, V.467, V.468, F.471 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.390, B:R.416, B:V.467, B:V.468, B:F.471 MPD.12: 7 residues within 4Å: Chain B: S.455, F.456, P.457, E.482, L.483, Y.484, W.571 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.456, B:W.571 Hydrogen bonds: B:S.455 Water bridges: B:E.482, B:E.482, B:E.482, B:E.482 MPD.13: 10 residues within 4Å: Chain B: F.341, Q.371, N.611, M.612, I.613, G.620, P.622, D.655, G.669, T.670 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.341, B:I.613, B:P.622 Hydrogen bonds: B:T.670

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 3 residues within 4Å: Chain A: E.375, F.429, L.432 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.375, A:F.429, A:L.432, H2O.7, H2O.10 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.7 CA.10: 3 residues within 4Å: Chain B: E.375, F.429, L.432 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.375, B:F.429, B:L.432, H2O.26, H2O.28 CA.11: 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

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

ACT.7: 4 residues within 4Å: Chain A: G.149, M.202, S.203, Q.204 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.204 Water bridges: A:D.144, A:M.202, A:Q.204 Salt bridges: A:H.383 ACT.14: 4 residues within 4Å: Chain B: G.149, M.202, S.203, Q.204 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.204 Water bridges: B:M.202, B:Q.204, B:H.383 Salt bridges: B:H.383

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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