SMTL ID : 7eiy.1

Human histidine decarboxylase mutant Y334F soaking with histidine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PLP.1: 14 residues within 4Å: Chain A: Y.85, T.153, V.154, S.155, H.198, G.250, T.252, D.277, A.279, N.306, K.309 Chain B: L.357, S.358 Ligands: HIS.2 11 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B, 2 Ligand-Ligand interactions Hydrogen bonds: A:V.154, A:S.155, A:N.306, B:S.358, B:S.358, B:S.358, H.2 Water bridges: A:S.308 Salt bridges: A:K.309 pi-Stacking: A:H.198 Hydrophobic interactions: H.2 PLP.4: 14 residues within 4Å: Chain A: L.357, S.358 Chain B: Y.85, T.153, V.154, S.155, H.198, G.250, T.252, D.277, A.279, N.306, K.309 Ligands: HIS.5 11 PLIP interactions: 6 interactions with chain B, 2 Ligand-Ligand interactions, 3 interactions with chain A Hydrogen bonds: B:V.154, B:S.155, B:S.155, B:N.306, H.5, A:S.358 Salt bridges: B:K.309 pi-Stacking: B:H.198 Hydrophobic interactions: H.5 Water bridges: A:S.358, A:S.358

2 x HIS: HISTIDINE(Non-covalent)

HIS.2: 12 residues within 4Å: Chain A: W.76, Y.84, Y.85, P.86, H.198, T.252, K.309 Chain B: L.106, F.108, L.357, S.358 Ligands: PLP.1 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.84, B:F.108 Hydrogen bonds: A:Y.85 Salt bridges: A:H.198 pi-Stacking: A:W.76 pi-Cation interactions: A:K.309 Water bridges: B:S.358 HIS.5: 12 residues within 4Å: Chain A: L.106, F.108, L.357, S.358 Chain B: W.76, Y.84, Y.85, P.86, H.198, T.252, K.309 Ligands: PLP.4 7 PLIP interactions: 2 Ligand-Ligand interactions, 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: H.5, H.5, A:S.358, B:Y.85, B:K.309 Hydrophobic interactions: A:F.108 Salt bridges: B:H.198

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 2 residues within 4Å: Chain A: R.16 Chain B: R.16 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:R.16, A:R.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Komori, H. et al., Structural analysis of the HDC Y334F mutant. J Biol Macromol (2021)

Release Date

2022-04-06

Peptides

Histidine decarboxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Histidine decarboxylase

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