SMTL ID : 4n20.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.66 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 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:V.259, A:L.458 Water bridges: B:L.303, A:L.458 MPD.2: 5 residues within 4Å: Chain A: Q.560, E.561, Y.564 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 Hydrogen bonds: A:H.600 Water bridges: 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 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.259, B:L.458 Water bridges: A:L.303, B:L.458 MPD.8: 5 residues within 4Å: Chain A: A.298, I.301 Chain B: Q.560, E.561, Y.564 6 PLIP interactions: 2 interactions with chain A, 4 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 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

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

ACT.4: 4 residues within 4Å: Chain A: S.106, T.107, E.108, 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: 4 residues within 4Å: Chain B: S.106, T.107, E.108, 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

4 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.3 CA.6: 4 residues within 4Å: Chain A: M.320, 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.9, H2O.18, H2O.25 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.32 CA.12: 4 residues within 4Å: Chain B: M.320, 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.38, H2O.47, H2O.55

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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