SMTL ID : 4n24.1

Crystal structure of Protein Arginine Deiminase 2 (100 uM Ca2+)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-dimer

Ligands

2 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.1: 5 residues within 4Å: Chain A: S.455, P.457, E.482, L.483, W.571 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.482, A:E.482, A:E.482 MRD.9: 5 residues within 4Å: Chain B: S.455, P.457, E.482, L.483, W.571 3 PLIP interactions: 3 interactions with chain B Water bridges: B:E.482, B:E.482, B:E.482

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

MPD.2: 5 residues within 4Å: Chain A: L.458 Chain B: E.220, Y.257, V.259, L.303 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.257, B:Y.257, B:V.259, B:L.303 MPD.8: 5 residues within 4Å: Chain A: D.280, L.390, S.392, R.416, V.467 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.416 Water bridges: A:D.280, A:F.471 MPD.10: 5 residues within 4Å: Chain A: E.220, Y.257, V.259, L.303 Chain B: L.458 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.257, A:Y.257, A:V.259, A:L.303 MPD.16: 5 residues within 4Å: Chain B: D.280, L.390, S.392, R.416, V.467 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:R.416 Water bridges: B:D.280, B:F.471

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 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.4: 3 residues within 4Å: Chain A: E.375, F.429, L.432 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.375, A:F.429, A:L.432, H2O.7, H2O.12, H2O.19 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.39 CA.12: 3 residues within 4Å: Chain B: E.375, F.429, L.432 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.375, B:F.429, B:L.432, H2O.29, H2O.33, H2O.40

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: M.320, T.321, E.375, F.376, V.672, R.674 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.321, A:T.321, A:T.321, A:E.375, A:F.376, A:V.672 Water bridges: A:E.375, A:V.672 GOL.6: 8 residues within 4Å: Chain A: F.341, R.368, Q.371, N.611, I.613, P.622, D.655, T.670 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.670, A:T.670 GOL.13: 6 residues within 4Å: Chain B: M.320, T.321, E.375, F.376, V.672, R.674 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.321, B:T.321, B:F.376, B:V.672 Water bridges: B:E.375, B:V.672 GOL.14: 8 residues within 4Å: Chain B: F.341, R.368, Q.371, N.611, I.613, P.622, D.655, T.670 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.655, B:T.670, B:T.670

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

ACT.7: 6 residues within 4Å: Chain A: G.149, V.151, M.202, S.203, Q.204, H.383 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.151, A:Q.204 Hydrogen bonds: A:Q.204, A:Q.204 Salt bridges: A:H.383 ACT.15: 6 residues within 4Å: Chain B: G.149, V.151, M.202, S.203, Q.204, H.383 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.151, B:Q.204 Hydrogen bonds: B:Q.204, B:Q.204 Water bridges: 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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