SMTL ID : 4n2d.1

Crystal structure of Protein Arginine Deiminase 2 (D123N, 0 mM Ca2+)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 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: 4 residues within 4Å: Chain A: E.561, M.596 Chain B: A.298, I.301 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:A.298, B:I.301, A:E.561 Water bridges: A:Q.560, A:Q.560 MPD.3: 4 residues within 4Å: Chain A: D.280, R.416, V.467, V.468 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.416, A:V.467, A:V.468 MPD.6: 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.7: 4 residues within 4Å: Chain A: A.298, I.301 Chain B: E.561, M.596 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:E.561, A:A.298, A:I.301 Water bridges: B:Q.560, B:Q.560 MPD.8: 4 residues within 4Å: Chain B: D.280, R.416, V.467, V.468 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:R.416, B:V.467, B:V.468

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 5 residues within 4Å: Chain A: N.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.146, A:D.148, A:V.150, A:E.152, H2O.9 CA.5: 3 residues within 4Å: Chain A: 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.8 CA.9: 5 residues within 4Å: Chain B: N.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.146, B:D.148, B:V.150, B:E.152, H2O.20 CA.10: 3 residues within 4Å: Chain B: 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.18

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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