SMTL ID : 7bqj.1

The structure of PdxI

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: H.161, F.204, Y.205, L.229, Q.412, V.416 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.161, A:Y.205, A:Y.205, A:Q.412 Water bridges: A:T.232 EDO.2: 4 residues within 4Å: Chain A: R.424, L.440, K.441, G.442 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.424, A:K.441 Water bridges: A:D.372 EDO.3: 6 residues within 4Å: Chain A: Q.14, V.17, N.45, R.48, A.49, L.52 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.14, A:Q.14, A:A.49

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: W.169, P.192, I.207 No protein-ligand interaction detected (PLIP) GOL.5: 6 residues within 4Å: Chain A: A.68, R.72 Chain B: R.38, M.148, D.152, T.238 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:R.72, A:R.72, B:R.38, B:D.152 Water bridges: B:T.238, B:T.238 GOL.6: 7 residues within 4Å: Chain A: Y.205, E.209, L.226, Y.230, E.288, R.289, Q.291 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.209, A:Y.230, A:Q.291 GOL.7: 7 residues within 4Å: Chain A: P.187, K.317, Y.318, K.337, E.338, P.339, K.342 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.317, A:Y.318, A:K.342 Water bridges: A:I.185, A:E.338, A:E.338 GOL.8: 4 residues within 4Å: Chain A: P.153, L.156, W.216, N.217 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.217 GOL.10: 7 residues within 4Å: Chain B: P.187, K.317, Y.318, K.337, E.338, P.339, K.342 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.317, B:Y.318, B:K.342, B:K.342 Water bridges: B:I.185, B:E.338 GOL.11: 7 residues within 4Å: Chain A: M.148, D.152, F.235, T.238, G.239 Chain B: A.68, R.72 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.238, B:R.72, B:R.72 Water bridges: A:R.38 GOL.12: 3 residues within 4Å: Chain B: P.153, W.216, N.217 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.217, B:N.217 GOL.13: 3 residues within 4Å: Chain B: W.169, P.192, I.207 No protein-ligand interaction detected (PLIP)

1 x NA: SODIUM ION(Non-functional Binders)

NA.9: 5 residues within 4Å: Chain A: G.265, Q.287, E.288, H.315, K.317 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.265, A:H.315 Water bridges: A:K.317

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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