SMTL ID : 7d8n.1

Structure of the inactive form of wild-type peptidylarginine deiminase type III (PAD3) crystallized under the condition with high concentrations of Ca2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-dimer

Ligands

10 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: D.165, D.168, H.170, D.176 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.165, A:D.168, A:H.170, H2O.1, H2O.1 CA.2: 5 residues within 4Å: Chain A: D.155, D.157, D.179, D.388 Ligands: CA.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.155, A:D.157, A:D.179, A:D.388, H2O.1 CA.3: 5 residues within 4Å: Chain A: Q.349, E.353, F.407, L.410, E.411 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.353, A:F.407, A:L.410, A:E.411, H2O.1 CA.4: 7 residues within 4Å: Chain A: N.153, D.155, D.157, D.165, D.176, D.179 Ligands: CA.2 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: 2 residues within 4Å: Chain A: R.372, E.395 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:R.372, A:E.395, H2O.2 CA.12: 5 residues within 4Å: Chain B: D.165, D.168, H.170, D.176, E.252 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.165, B:D.168, B:H.170 CA.13: 5 residues within 4Å: Chain B: D.155, D.157, D.179, D.388 Ligands: CA.15 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.155, B:D.157, B:D.157, B:D.179, B:D.388 CA.14: 4 residues within 4Å: Chain B: E.353, F.407, L.410, E.411 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.353, B:F.407, B:L.410, B:E.411, H2O.3 CA.15: 7 residues within 4Å: Chain B: N.153, D.155, D.157, D.165, D.176, D.179 Ligands: CA.13 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.155, B:D.157, B:D.165, B:D.176, B:D.179 CA.16: 2 residues within 4Å: Chain B: R.372, E.395 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:R.372, B:E.395, H2O.4

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: S.16, V.18, H.197, D.273, S.275 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.273, A:S.275 GOL.7: 3 residues within 4Å: Chain A: S.160, H.172, E.224 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.160, A:S.160, A:E.224 GOL.9: 6 residues within 4Å: Chain A: R.8, D.28 Chain B: S.492, A.495, K.498, D.568 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.8, A:R.8, A:D.28, B:S.492, B:D.568 Water bridges: A:D.28 GOL.10: 2 residues within 4Å: Chain A: E.502 Chain B: E.35 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.35 GOL.11: 3 residues within 4Å: Chain B: D.158, S.160, H.172 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.160, B:H.172 GOL.17: 6 residues within 4Å: Chain B: S.16, A.17, D.196, H.197, D.273, S.275 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.273, B:S.275 GOL.18: 1 residues within 4Å: Chain B: D.28 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.74

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

CL.8: 2 residues within 4Å: Chain A: E.307, K.333 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain B: E.307, K.333 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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