SMTL ID : 8ql0.1

Structure of human PAD6 Phosphomimic mutant V10E/S446E, apo

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

homo-dimer

Ligands

8 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.1: 9 residues within 4Å: Chain A: F.327, R.354, Q.357, R.618, I.620, C.665, Y.666, C.674, A.675 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.618, A:R.618 Water bridges: A:M.619 PEG.2: 7 residues within 4Å: Chain A: E.559, E.562, K.563, H.566 Chain B: F.10, Q.11, L.292 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.559, A:H.566 PEG.4: 6 residues within 4Å: Chain A: A.143, K.146, I.148, W.154 Chain B: Q.427 Ligands: 1PE.6 No protein-ligand interaction detected (PLIP) PEG.5: 5 residues within 4Å: Chain A: T.371, V.682, P.683, F.684, A.685 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.371 PEG.8: 9 residues within 4Å: Chain B: F.327, R.354, Q.357, R.618, I.620, C.665, Y.666, C.674, A.675 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.618, B:R.618 Water bridges: B:M.619 PEG.9: 7 residues within 4Å: Chain A: F.10, Q.11, L.292 Chain B: E.559, E.562, K.563, H.566 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.559 PEG.11: 6 residues within 4Å: Chain A: Q.427 Chain B: A.143, K.146, I.148, W.154 Ligands: 1PE.13 No protein-ligand interaction detected (PLIP) PEG.12: 5 residues within 4Å: Chain B: T.371, V.682, P.683, F.684, A.685 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.371

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: P.506, S.507, Y.510, R.514, K.555, N.558, E.559, E.562 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.514, A:K.555, A:E.559, A:E.562, A:E.562 GOL.10: 8 residues within 4Å: Chain B: P.506, S.507, Y.510, R.514, K.555, N.558, E.559, E.562 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.514, B:K.555, B:E.562

2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.6: 8 residues within 4Å: Chain A: K.146 Chain B: V.426, Q.427, K.429, Y.431, T.574, E.575 Ligands: PEG.4 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.146 Water bridges: B:R.435 1PE.13: 8 residues within 4Å: Chain A: V.426, Q.427, K.429, Y.431, T.574, E.575 Chain B: K.146 Ligands: PEG.11 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Water bridges: A:Y.431, A:Y.431, A:R.435 Hydrogen bonds: B:K.146

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

CL.7: 2 residues within 4Å: Chain A: R.300, Q.463 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain B: R.300, Q.463 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ranaivoson, F.M. et al., Crystal structure of human peptidylarginine deiminase type VI (PAD6) provides insights into its inactivity. Iucrj (2024)

Release Date

2024-05-08

Peptides

Protein-arginine deiminase type-6: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Protein-arginine deiminase type-6