SMTL ID : 7bqk.1

The structure of PdxI in complex with its substrate analogue

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 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: 14 residues within 4Å: Chain A: W.158, H.161, F.204, Y.205, L.229, F.236, T.333, H.336, K.337, I.366, I.409, Q.412, V.413 Chain B: M.76 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.236, A:T.333, A:I.366, A:I.409, A:Q.412 Hydrogen bonds: A:H.161, A:K.337, A:K.337, A:Q.412 F56.9: 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.333, H.336, K.337, I.366, I.409, Q.412, V.413 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.236, B:I.242, B:T.333, B:I.366, B:I.409, B:Q.412 Hydrogen bonds: B:H.161, B:K.337, B:K.337, B:Q.412 Water bridges: B:D.233

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

EDO.2: 3 residues within 4Å: Chain A: W.169, P.192, K.202 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.202, A:K.202 EDO.3: 4 residues within 4Å: Chain A: Y.205, K.317, K.337 Ligands: GOL.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.317, A:K.337 Water bridges: A:K.317 EDO.4: 3 residues within 4Å: Chain A: P.153, W.216, N.217 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.217 EDO.5: 6 residues within 4Å: Chain A: P.356, N.357, K.358, S.359, R.360, I.457 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.356 Water bridges: A:R.360, A:L.458 EDO.10: 5 residues within 4Å: Chain A: P.168, N.172 Chain B: P.168, N.172, K.173 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:P.168, A:P.168 EDO.11: 3 residues within 4Å: Chain B: W.169, P.192, K.202 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.202, B:K.202 EDO.12: 4 residues within 4Å: Chain B: Y.205, K.317, K.337 Ligands: GOL.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.337 Water bridges: B:K.317 EDO.13: 4 residues within 4Å: Chain B: P.356, N.357, K.358, S.359 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.356 Water bridges: B:R.360

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 8 residues within 4Å: Chain A: P.187, K.317, Y.318, K.337, E.338, P.339, K.342 Ligands: EDO.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.317, A:K.342, A:K.342 Water bridges: A:I.185, A:I.185, A:E.338, A:E.338, A:K.342 GOL.7: 9 residues within 4Å: Chain A: L.51, A.394, L.396, I.402, Q.445, T.446, V.447, G.448, N.449 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.448, A:G.448 Water bridges: A:G.371 GOL.8: 6 residues within 4Å: Chain A: N.62, I.65, N.70, H.74 Chain B: Q.129, Y.131 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.131, A:H.74 GOL.14: 7 residues within 4Å: Chain B: P.187, Y.318, K.337, E.338, P.339, K.342 Ligands: EDO.12 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.318, B:Y.318 Water bridges: B:I.185, B:K.317, B:K.337, B:E.338

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

Methyltransf_2 domain-containing protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Methyltransf_2 domain-containing protein

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