SMTL ID : 4n2m.1

Crystal structure of Protein Arginine Deiminase 2 (E354A, 0 mM Ca2+)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 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 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.259, A:L.458 Water bridges: B:L.303 MPD.2: 5 residues within 4Å: Chain A: E.561, Y.564, M.596 Chain B: A.298, I.301 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:E.561, A:Y.564, B:A.298, B:I.301 Water bridges: A:Q.560, A:Q.560, A:Q.560 MPD.3: 7 residues within 4Å: Chain A: D.280, L.390, R.416, F.429, V.467, V.468, F.471 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.390, A:R.416, A:F.429, A:V.467, A:V.468, A:F.471 MPD.6: 6 residues within 4Å: Chain A: S.455, F.456, P.457, E.482, L.483, W.571 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.456 Hydrogen bonds: A:S.455 Water bridges: A:S.454 MPD.7: 5 residues within 4Å: Chain A: E.220, Y.257, V.259, L.303 Chain B: L.458 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.259, B:L.458 Water bridges: A:L.303 MPD.8: 5 residues within 4Å: Chain A: A.298, I.301 Chain B: E.561, Y.564, M.596 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:A.298, A:I.301, B:E.561, B:Y.564 Water bridges: B:Q.560, B:Q.560, B:Q.560 MPD.9: 7 residues within 4Å: Chain B: D.280, L.390, R.416, F.429, V.467, V.468, F.471 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.390, B:R.416, B:F.429, B:V.467, B:V.468, B:F.471 MPD.12: 6 residues within 4Å: Chain B: S.455, F.456, P.457, E.482, L.483, W.571 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.456 Hydrogen bonds: B:S.455 Water bridges: B:S.454, B:E.482

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

ACT.4: 6 residues within 4Å: Chain A: S.106, T.107, E.108, S.110, T.135, P.212 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.212 Hydrogen bonds: A:E.108 Water bridges: A:D.112 ACT.10: 6 residues within 4Å: Chain B: S.106, T.107, E.108, S.110, T.135, P.212 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.212 Hydrogen bonds: B:E.108 Water bridges: B:S.106

2 x CA: CALCIUM ION(Non-covalent)

CA.5: 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.6 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.31

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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