SMTL ID : 4n2n.1

Crystal structure of Protein Arginine Deiminase 2 (E354A, 10 mM Ca2+)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

MPD.1: 8 residues within 4Å: Chain A: Y.237, E.239, H.258, V.259, V.260, K.261, L.269, F.271 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.237, A:K.261, A:L.269 MPD.2: 7 residues within 4Å: Chain A: S.454, 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, A:E.482 Hydrogen bonds: A:S.455 MPD.3: 4 residues within 4Å: Chain B: E.220, Y.257, V.259, L.303 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.257, B:V.259, B:L.303 MPD.10: 8 residues within 4Å: Chain B: Y.237, E.239, H.258, V.259, V.260, K.261, L.269, F.271 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.237, B:K.261, B:L.269 MPD.11: 7 residues within 4Å: Chain B: S.454, S.455, F.456, P.457, E.482, L.483, W.571 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.456, B:E.482 Hydrogen bonds: B:S.455 MPD.12: 4 residues within 4Å: Chain A: E.220, Y.257, V.259, L.303 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.257, A:V.259, A:L.303

8 x CA: CALCIUM ION(Non-covalent)

CA.4: 6 residues within 4Å: Chain A: D.177, E.179, D.201, K.384, D.410 Ligands: CA.5 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.177, A:E.179, A:D.410, H2O.3, H2O.3 CA.5: 7 residues within 4Å: Chain A: N.175, D.177, E.179, D.187, D.198, D.201 Ligands: CA.4 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.177, A:E.179, A:D.187, A:D.198, A:D.201 CA.6: 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.17 CA.9: 3 residues within 4Å: Chain A: D.187, D.190, K.192 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.187, A:K.192, H2O.7, H2O.12, H2O.22 CA.13: 6 residues within 4Å: Chain B: D.177, E.179, D.201, K.384, D.410 Ligands: CA.14 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.177, B:E.179, B:D.410, H2O.28, H2O.29 CA.14: 7 residues within 4Å: Chain B: N.175, D.177, E.179, D.187, D.198, D.201 Ligands: CA.13 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.177, B:E.179, B:D.187, B:D.198, B:D.201 CA.15: 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.42 CA.18: 3 residues within 4Å: Chain B: D.187, D.190, K.192 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.187, B:K.192, H2O.32, H2O.38, H2O.47

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

ACT.7: 5 residues within 4Å: Chain A: G.33, S.34, R.35, D.128, Q.129 No protein-ligand interaction detected (PLIP) ACT.8: 1 residues within 4Å: Chain B: I.301 No protein-ligand interaction detected (PLIP) ACT.16: 5 residues within 4Å: Chain B: G.33, S.34, R.35, D.128, Q.129 No protein-ligand interaction detected (PLIP) ACT.17: 1 residues within 4Å: Chain A: I.301 No protein-ligand interaction detected (PLIP)

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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