SMTL ID : 7d56.1 (1 other biounit)

Structure of the peptidylarginine deiminase type III (PAD3) in complex with Cl-amidine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.17 Å

Oligo State

homo-dimer

Ligands

2 x BFB: N-[(1S)-1-(AMINOCARBONYL)-4-(ETHANIMIDOYLAMINO)BUTYL]BENZAMIDE(Covalent)

BFB.1: 9 residues within 4Å: Chain A: W.347, D.350, V.468, H.470, D.472, N.589, L.640, H.641, C.646 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.347, A:V.468, A:L.640 Hydrogen bonds: A:D.350, A:H.470, A:H.641 BFB.13: 9 residues within 4Å: Chain B: W.347, D.350, V.468, H.470, D.472, N.589, L.640, H.641, C.646 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.347, B:V.468, B:L.640 Hydrogen bonds: B:D.350, B:H.641

10 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: Q.349, E.353, F.407, L.410, E.411 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.353, A:F.407, A:L.410, A:E.411 CA.3: 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.4: 5 residues within 4Å: Chain A: D.155, D.157, D.179, P.387, 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.5: 4 residues within 4Å: Chain A: E.351, D.369, S.370, N.373 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.351, A:D.369, A:D.369, A:S.370 CA.6: 4 residues within 4Å: Chain A: D.165, D.168, H.170, D.176 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.168, A:D.168 CA.14: 5 residues within 4Å: Chain B: Q.349, E.353, F.407, L.410, E.411 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.353, B:F.407, B:L.410, B:E.411 CA.15: 6 residues within 4Å: Chain B: N.153, D.155, D.157, D.165, D.176, D.179 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: 5 residues within 4Å: Chain B: D.155, D.157, D.179, P.387, 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.17: 4 residues within 4Å: Chain B: E.351, D.369, S.370, N.373 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.351, B:D.369, B:D.369, B:S.370 CA.18: 4 residues within 4Å: Chain B: D.165, D.168, H.170, D.176 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.168, B:D.168

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

CL.7: 2 residues within 4Å: Chain A: V.7, Y.30 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain A: R.8 Chain B: S.492, Q.545, D.568 Ligand excluded by PLIP CL.9: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain A: G.516, F.603 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain B: V.7, Y.30 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain A: S.492, Q.545, D.568 Chain B: R.8 Ligand excluded by PLIP CL.21: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain B: G.516, F.603 Ligand excluded by PLIP

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.12: 6 residues within 4Å: Chain A: E.41, V.42, Y.43, D.64, T.65, R.66 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.42 EDO.23: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.24: 6 residues within 4Å: Chain B: E.41, V.42, Y.43, D.64, T.65, R.66 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.42

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
C

B
C

Protein-arginine deiminase type-3

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