SMTL ID : 6omq.1

Crystal structure of PtmU3 complexed with PTM substrate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

homo-dimer

Ligands

9 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: 6 residues within 4Å: Chain A: N.7, W.83, R.340, T.344, V.349, L.352 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:T.344, A:V.349 Hydrogen bonds: A:N.7, A:N.7 Water bridges: A:R.340, A:T.344 Salt bridges: A:R.340 ACT.3: 4 residues within 4Å: Chain A: V.36, T.43, Y.45, R.53 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.45 Hydrogen bonds: A:Y.45, A:R.53 Water bridges: A:D.38, A:T.43 ACT.4: 4 residues within 4Å: Chain A: R.318, E.321, V.322, E.325 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.325 Salt bridges: A:R.318 ACT.5: 5 residues within 4Å: Chain A: K.116, L.120, L.150, G.151, Y.152 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.120, A:Y.152 Water bridges: A:L.126, A:Q.153 Salt bridges: A:K.116 ACT.9: 8 residues within 4Å: Chain B: N.7, W.83, R.340, T.344, V.349, P.350, A.351, L.352 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:T.344, B:V.349 Hydrogen bonds: B:N.7, B:L.352, B:L.352 Water bridges: B:R.340 Salt bridges: B:R.340 ACT.10: 6 residues within 4Å: Chain A: E.166, N.168, M.169 Chain B: A.199, R.200, G.201 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.200, B:G.201, A:N.168 Hydrophobic interactions: A:E.166 ACT.11: 2 residues within 4Å: Chain B: F.316, P.317 4 PLIP interactions: 4 interactions with chain B Water bridges: B:D.79, B:D.79, B:Q.80, B:Q.80 ACT.12: 5 residues within 4Å: Chain B: K.116, L.120, L.150, G.151, Y.152 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.120, B:Y.152 Hydrogen bonds: B:L.150 Water bridges: B:K.116 Salt bridges: B:K.116

7 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)

MN.6: 6 residues within 4Å: Chain A: D.10, H.12, H.189, E.241, D.308 Ligands: MN.7 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.7: 5 residues within 4Å: Chain A: E.241, D.308, H.311, E.313 Ligands: MN.6 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.10 MN.8: 3 residues within 4Å: Chain A: L.312, G.314 Chain B: Q.260 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:L.312, A:G.314, H2O.6, H2O.10, H2O.27 MN.14: 6 residues within 4Å: Chain B: D.10, H.12, H.189, E.241, D.308 Ligands: MN.15 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.15: 5 residues within 4Å: Chain B: E.241, D.308, H.311, E.313 Ligands: MN.14 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.241, B:D.308, B:H.311, B:E.313, H2O.26 MN.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MN.17: 3 residues within 4Å: Chain A: Q.260 Chain B: L.312, G.314 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:L.312, B:G.314, H2O.12, H2O.17, H2O.27

1 x MZD: S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] (5beta,7alpha,8alpha,10alpha,11alpha,13alpha)-7-hydroxy-11,16-epoxykaurane-18-thioate(Non-covalent)

MZD.13: 18 residues within 4Å: Chain A: H.261, F.264 Chain B: R.52, D.54, M.62, S.90, L.93, I.190, G.191, T.196, V.197, A.199, R.200, G.204, A.205, N.208, Y.209, E.313 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.93, B:I.190, B:T.196, A:F.264 Hydrogen bonds: B:R.52, B:R.52, B:G.191, B:N.208

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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