SMTL ID : 7bqo.1

The structure of HpiI in complex with its substrate analogue

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.53 Å

Oligo State

homo-dimer

Ligands

2 x F56: 3-[(E,2S,4S)-2,4-dimethyloct-6-enoyl]-4-oxidanyl-1H-pyridin-2-one(Non-covalent)

F56.1: 15 residues within 4Å: Chain A: W.158, H.161, F.204, Y.205, L.229, F.236, I.242, T.335, H.338, K.339, I.368, I.411, Q.414, M.415 Chain B: M.76 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.236, A:I.242, A:T.335, A:I.368, A:I.411, A:Q.414 Hydrogen bonds: A:H.161, A:Y.205, A:Q.414 Water bridges: A:D.233 F56.5: 15 residues within 4Å: Chain A: M.76 Chain B: W.158, H.161, F.204, Y.205, L.229, F.236, I.242, T.335, H.338, K.339, I.368, I.411, Q.414, M.415 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.236, B:I.242, B:T.335, B:I.368, B:I.411, B:Q.414 Hydrogen bonds: B:H.161, B:Y.205, B:Y.205, B:Q.414 Water bridges: B:K.339

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.2: 3 residues within 4Å: Chain A: W.169, P.192, I.207 2 PLIP interactions: 2 interactions with chain A pi-Stacking: A:W.169, A:W.169 IMD.6: 3 residues within 4Å: Chain B: W.169, P.192, I.207 2 PLIP interactions: 2 interactions with chain B pi-Stacking: B:W.169, B:W.169

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: Y.205, K.319, Y.320, K.339, E.340 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.319, A:K.319, A:Y.320 GOL.7: 5 residues within 4Å: Chain B: Y.205, K.319, Y.320, K.339, E.340 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.319, B:K.319 Water bridges: B:E.340

2 x B3P: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

B3P.4: 1 residues within 4Å: Chain A: E.215 No protein-ligand interaction detected (PLIP) B3P.8: 1 residues within 4Å: Chain B: E.215 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ohashi, M. et al., An enzymatic Alder-ene reaction. Nature (2020)

Release Date

2020-10-14

Peptides

HpiI: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

HpiI

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