SMTL ID : 6omp.1

Crystal structure of apo PtmU3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

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

ACT.1: 5 residues within 4Å: Chain A: K.116, L.120, L.150, G.151, Y.152 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.120, A:Y.152 Water bridges: A:K.116, A:K.116, A:L.126, A:Q.153 Salt bridges: A:K.116 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: 9 residues within 4Å: Chain A: R.73, D.76, L.77, Q.80, I.82, E.85, S.307, Y.309, F.316 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:D.76, A:Q.80, A:I.82, A:Y.309, A:F.316 Hydrogen bonds: A:S.307, A:S.307 Salt bridges: A:R.73 ACT.4: 3 residues within 4Å: Chain A: R.318, E.321, E.325 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.318 Salt bridges: A:R.318 ACT.5: 2 residues within 4Å: Chain A: D.331, P.332 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.331 Water bridges: A:G.329, A:D.331 ACT.10: 3 residues within 4Å: Chain B: S.123, P.124, R.125 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.123 Salt bridges: B:R.125 ACT.11: 5 residues within 4Å: Chain B: K.116, L.120, L.150, G.151, Y.152 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:K.116, B:L.120, B:Y.152 Hydrogen bonds: B:L.150 Water bridges: B:Q.153 Salt bridges: B:K.116 ACT.12: 8 residues within 4Å: Chain B: N.7, W.83, R.340, T.344, V.349, P.350, A.351, L.352 8 PLIP interactions: 8 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, B:R.340 Salt bridges: B:R.340 ACT.13: 8 residues within 4Å: Chain B: R.73, L.77, Q.80, I.82, E.85, S.307, Y.309, F.316 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:R.73, B:L.77, B:Y.309 Hydrogen bonds: B:E.85, B:S.307 ACT.14: 7 residues within 4Å: Chain A: E.166, N.168, M.169 Chain B: V.198, A.199, R.200, G.201 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:E.166 Hydrogen bonds: A:N.168, B:V.198, B:R.200, B:G.201

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

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.11 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.4, H2O.10, H2O.34 MN.9: 1 residues within 4Å: Chain A: D.38 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.38, H2O.2, H2O.12 MN.15: 6 residues within 4Å: Chain B: D.10, H.12, H.189, E.241, D.308 Ligands: MN.16 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.16: 5 residues within 4Å: Chain B: E.241, D.308, H.311, E.313 Ligands: MN.15 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.30 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.13, H2O.27, H2O.32

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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