SMTL ID : 7d5v.1

Structure of the C646A mutant of peptidylarginine deiminase type III (PAD3)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: E.24, S.53, G.59, R.60 Ligand excluded by PLIP EDO.2: 3 residues within 4Å: Chain A: W.68, R.69 Ligands: EDO.9 Ligand excluded by PLIP EDO.3: 2 residues within 4Å: Chain A: H.91, Y.111 Ligand excluded by PLIP EDO.4: 5 residues within 4Å: Chain A: T.299, E.353, L.354, G.355, R.652 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: S.492, G.494, A.495, K.498, D.568 Chain B: R.8 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: F.497, Q.501, I.538, K.542 Chain B: Y.30, G.31 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: Q.4, R.5 Chain B: W.550, V.554, R.557 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: W.550, V.554, R.557 Chain B: Q.4 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: I.52, P.54, E.61 Ligands: EDO.2 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: D.536, L.537, Y.540, K.574, T.575 Ligand excluded by PLIP EDO.11: 7 residues within 4Å: Chain A: R.67, H.97, S.98, S.99, E.101, P.102, L.103 Ligand excluded by PLIP EDO.12: 2 residues within 4Å: Chain A: P.365, C.651 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: D.28, F.40, F.70, D.71, L.74 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain A: R.8, D.28 Chain B: R.552, E.563 Ligands: EDO.20 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain B: R.510, S.527, N.529, Q.530 Ligand excluded by PLIP EDO.20: 7 residues within 4Å: Chain A: R.8 Chain B: S.492, A.495, K.498, R.552, D.568 Ligands: EDO.14 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain B: L.11, A.106, Y.107 Ligand excluded by PLIP EDO.22: 2 residues within 4Å: Chain B: D.49, R.62 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain A: Y.30, G.31 Chain B: F.497, Q.501, I.538, K.542 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain B: Q.4, E.24, S.53, G.59, R.60 Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain B: D.536, L.537, Y.540, K.574, T.575 Ligand excluded by PLIP EDO.26: 3 residues within 4Å: Chain B: H.91, Q.93, Y.111 Ligand excluded by PLIP EDO.27: 7 residues within 4Å: Chain B: R.67, H.97, S.98, S.99, E.101, P.102, L.103 Ligand excluded by PLIP EDO.28: 7 residues within 4Å: Chain B: L.306, Y.356, T.363, P.365, C.651, R.652, P.654 Ligand excluded by PLIP EDO.29: 5 residues within 4Å: Chain B: E.41, V.42, D.64, T.65, R.66 Ligand excluded by PLIP

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.15: 4 residues within 4Å: Chain A: S.16, D.273, S.275, N.276 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.273, A:S.275, A:S.275, A:N.276 Water bridges: A:S.16, A:S.16 GOL.16: 7 residues within 4Å: Chain A: E.178, D.179, K.362, L.364, P.387, D.388, F.389 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.178, A:K.362, A:F.389 GOL.17: 5 residues within 4Å: Chain A: N.153, C.154, Q.212, E.252, L.254 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.153, A:Q.212 Water bridges: A:D.176 GOL.18: 4 residues within 4Å: Chain A: E.41, V.42, D.64, R.66 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.41, A:V.42, A:V.42, A:R.66 Water bridges: A:R.66 GOL.30: 4 residues within 4Å: Chain B: S.16, D.273, S.275, N.276 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.16, B:D.273, B:S.275, B:S.275, B:N.276 Water bridges: B:S.16, B:D.273 GOL.31: 6 residues within 4Å: Chain B: N.153, D.176, E.178, D.179, K.362, D.388 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.178, B:E.178, B:P.387 GOL.32: 5 residues within 4Å: Chain B: N.153, C.154, E.252, G.253, L.254 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:C.154, B:Q.212, B:E.252, B:G.253 GOL.33: 8 residues within 4Å: Chain B: D.28, F.40, F.70, D.71, A.72, L.74, I.76, Y.96 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.71, B:L.74, B:Y.96

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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