SMTL ID : 6omr.1

Crystal structure of PtmU3 complexed with PTN substrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-dimer

Ligands

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 8 residues within 4Å: Chain A: R.73, D.76, L.77, Q.80, I.82, E.85, S.307, Y.309 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:R.73, A:L.77, A:Y.309 Hydrogen bonds: A:D.76, A:S.307 ACT.2: 5 residues within 4Å: Chain A: N.7, W.83, R.340, T.344, V.349 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.344, A:V.349 Hydrogen bonds: A:N.7, A:N.7 Salt bridges: A:R.340 ACT.3: 5 residues within 4Å: Chain A: K.116, L.120, L.150, G.151, Y.152 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.120, A:Y.152 Water bridges: A:L.126 Salt bridges: A:K.116 ACT.7: 7 residues within 4Å: Chain B: N.7, R.340, T.344, V.349, P.350, A.351, L.352 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:T.344, B:V.349 Hydrogen bonds: B:N.7, B:L.352, B:L.352 Salt bridges: B:R.340

5 x MN: MANGANESE (II) ION(Non-covalent)

MN.4: 6 residues within 4Å: Chain A: D.10, H.12, H.189, E.241, D.308 Ligands: MN.5 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.10, A:H.12, A:H.189, A:E.241, A:D.308 MN.5: 5 residues within 4Å: Chain A: E.241, D.308, H.311, E.313 Ligands: MN.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.241, A:D.308, A:H.311, A:E.313, H2O.5 MN.6: 1 residues within 4Å: Chain A: D.38 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.38 MN.9: 5 residues within 4Å: Chain B: D.10, H.12, H.189, E.241, D.308 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.10, B:H.12, B:H.189, B:E.241, B:D.308 MN.10: 5 residues within 4Å: Chain B: E.241, D.308, H.311, E.313 Ligands: MYM.8 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.241, B:E.241, B:D.308, B:H.311, B:E.313

1 x MYM: S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] (5beta,7alpha,8alpha,10alpha,12alpha)-7-hydroxyatis-16-ene-18-thioate(Non-covalent)

MYM.8: 20 residues within 4Å: Chain A: F.264 Chain B: R.52, M.62, S.90, L.93, W.94, I.190, G.191, T.196, V.197, A.199, R.200, G.204, A.205, N.208, Y.209, T.212, E.241, E.313 Ligands: MN.10 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.93, B:W.94, B:I.190, A:F.264 Hydrogen bonds: B:R.52, B:R.52, B:G.191, B:N.208 Water bridges: B:R.200, B:R.200 Salt bridges: B:R.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dong, L.B. et al., Characterization and Crystal Structure of a Nonheme Diiron Monooxygenase Involved in Platensimycin and Platencin Biosynthesis. J.Am.Chem.Soc. (2019)

Release Date

2019-07-24

Peptides

PtmU3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PtmU3

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