SMTL ID : 7d5r.1

Structure of the Ca2+-bound C646A mutant of peptidylarginine deiminase type III (PAD3)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.15 Å

Oligo State

homo-dimer

Ligands

10 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: D.155, D.157, Q.175, D.179, K.362, D.388 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.157, A:D.157, A:D.179, A:D.179, A:D.388 CA.2: 5 residues within 4Å: Chain A: Q.349, E.353, F.407, L.410, E.411 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:F.407, A:L.410, A:E.411 CA.3: 6 residues within 4Å: Chain A: E.351, D.369, S.370, R.372, N.373, E.395 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.369, A:D.369, A:S.370 CA.4: 6 residues within 4Å: Chain A: N.153, D.155, D.157, D.165, D.176, D.179 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.155, A:D.157, A:D.165, A:D.176, A:D.179 CA.5: 4 residues within 4Å: Chain A: D.165, D.168, H.170, D.176 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.165, A:D.168, A:D.168, A:D.176 CA.9: 5 residues within 4Å: Chain B: D.155, D.157, D.179, K.362, D.388 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.157, B:D.157, B:D.179, B:D.179, B:D.388 CA.10: 5 residues within 4Å: Chain B: Q.349, E.353, F.407, L.410, E.411 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:F.407, B:L.410, B:E.411 CA.11: 6 residues within 4Å: Chain B: E.351, D.369, S.370, R.372, N.373, E.395 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.369, B:D.369, B:S.370 CA.12: 6 residues within 4Å: Chain B: N.153, D.155, D.157, D.165, D.176, D.179 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.157, B:D.165, B:D.176 CA.13: 5 residues within 4Å: Chain B: D.165, D.168, H.170, V.171, D.176 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.168, B:D.168, B:D.176

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: R.8, D.28, N.55, A.72, L.74, E.75 Chain B: R.552 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.8, A:N.55, A:A.72, A:E.75 GOL.14: 6 residues within 4Å: Chain A: E.563 Chain B: D.28, N.55, A.72, L.74, E.75 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.28, B:D.28, B:N.55, B:E.75, B:E.75

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 3 residues within 4Å: Chain A: S.492, K.498 Chain B: R.8 Ligand excluded by PLIP CL.8: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.15: 1 residues within 4Å: Chain B: K.505 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain A: V.33, F.70 Chain B: K.498 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Funabashi, K. et al., Structures of human peptidylarginine deiminase type III provide insights into substrate recognition and inhibitor design. Arch.Biochem.Biophys. (2021)

Release Date

2021-06-02

Peptides

Protein-arginine deiminase type-3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protein-arginine deiminase type-3

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