SMTL ID : 4n22.1

Crystal structure of Protein Arginine Deiminase 2 (50 uM Ca2+)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-dimer

Ligands

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

ACT.1: 3 residues within 4Å: Chain A: R.469, K.473, E.482 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.473 Salt bridges: A:R.469 ACT.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ACT.3: 7 residues within 4Å: Chain A: D.144, G.149, V.151, M.202, S.203, Q.204, H.383 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:M.202, A:Q.204 Water bridges: A:Q.204, A:H.383, A:H.383 Salt bridges: A:H.383 ACT.8: 3 residues within 4Å: Chain B: R.469, K.473, E.482 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:K.473 Water bridges: B:E.482 Salt bridges: B:R.469 ACT.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ACT.10: 7 residues within 4Å: Chain B: D.144, G.149, V.151, M.202, S.203, Q.204, H.383 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:M.202, B:Q.204 Water bridges: B:Q.204 Salt bridges: B:H.383

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: M.320, T.321, E.375, F.376, N.671, V.672 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.321, A:T.321, A:E.375, A:F.376, A:V.672 Water bridges: A:E.375 GOL.11: 6 residues within 4Å: Chain B: M.320, T.321, E.375, F.376, N.671, V.672 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.321, B:F.376, B:V.672 Water bridges: B:T.321, B:E.375

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.18 CA.6: 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.9, H2O.15, H2O.18 CA.12: 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.37 CA.13: 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.28, H2O.34, H2O.37

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

MPD.7: 6 residues within 4Å: Chain A: S.455, F.456, P.457, E.482, L.483, W.571 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.482 Hydrogen bonds: A:S.455 MPD.14: 6 residues within 4Å: Chain B: S.455, F.456, P.457, E.482, L.483, W.571 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:E.482 Hydrogen bonds: B:S.455

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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