SMTL ID : 4n2k.1

Crystal structure of Protein Arginine Deiminase 2 (Q350A, 0 mM Ca2+)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

homo-dimer

Ligands

6 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: 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:V.259, A:L.458 Water bridges: A:L.458 MPD.2: 6 residues within 4Å: Chain A: Q.560, E.561, Y.564, M.596 Chain B: A.298, I.301 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:A.298, B:I.301, A:E.561, A:Y.564 Water bridges: A:Q.560, A:Q.560, A:Q.560 MPD.3: 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.7: 5 residues within 4Å: Chain A: E.220, Y.257, V.259, L.303 Chain B: L.458 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.259, B:L.458 Water bridges: B:L.458 MPD.8: 6 residues within 4Å: Chain A: A.298, I.301 Chain B: Q.560, E.561, Y.564, M.596 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:E.561, B:Y.564, A:A.298, A:I.301 Water bridges: B:Q.560, B:Q.560, B:Q.560 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

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 4 residues within 4Å: Chain A: M.320, E.375, F.429, L.432 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.375, A:F.429, A:L.432, H2O.12 CA.5: 5 residues within 4Å: Chain A: D.144, D.146, D.148, V.150, E.152 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.144, A:D.146, A:V.150, A:E.152, H2O.3 CA.10: 4 residues within 4Å: Chain B: M.320, E.375, F.429, L.432 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.375, B:F.429, B:L.432, H2O.40 CA.11: 5 residues within 4Å: Chain B: D.144, D.146, D.148, V.150, E.152 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.144, B:D.146, B:V.150, B:E.152, H2O.30

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: M.320, T.321, N.323, E.375, F.376, N.671, V.672 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.321, A:E.375, A:F.376, A:F.376, A:V.672 Water bridges: A:E.375, A:L.432 GOL.12: 7 residues within 4Å: Chain B: M.320, T.321, N.323, E.375, F.376, N.671, V.672 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:F.376, B:F.376, B:V.672 Water bridges: B:T.321, B:E.375, B:L.432

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

Related Entries With Identical Sequence