SMTL ID : 4xcb.1

Crystal Structure of HygX from Streptomyces hygroscopicus with nickel, 2-oxoglutarate, and hygromycin B bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

4 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 3 residues within 4Å: Chain A: H.105, H.209 Ligands: AKG.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.105, A:H.209, H2O.3, H2O.3 NI.4: 3 residues within 4Å: Chain B: H.105, H.209 Ligands: AKG.5 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.105, B:H.209, H2O.10, H2O.10 NI.7: 5 residues within 4Å: Chain C: H.105, K.140, H.209 Ligands: AKG.8, HY0.9 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.105, C:H.209, H2O.17, H2O.17 NI.10: 5 residues within 4Å: Chain D: H.105, K.140, H.209 Ligands: AKG.11, HY0.12 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.105, D:H.209, H2O.21, H2O.21

4 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.2: 14 residues within 4Å: Chain A: Y.92, L.94, L.102, H.105, K.140, L.142, Y.144, F.156, H.209, T.211, R.220, L.222 Ligands: NI.1, HY0.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.102, A:L.142, A:F.156 Hydrogen bonds: A:Y.92, A:Y.144 Water bridges: A:R.96 Salt bridges: A:H.105, A:K.140, A:R.220 AKG.5: 14 residues within 4Å: Chain B: Y.92, L.94, L.102, H.105, K.140, L.142, Y.144, F.156, H.209, T.211, R.220, L.222 Ligands: NI.4, HY0.6 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.102, B:L.142, B:F.156 Water bridges: B:R.96 Salt bridges: B:H.105, B:K.140, B:R.220 AKG.8: 14 residues within 4Å: Chain C: Y.92, L.94, L.102, H.105, K.140, L.142, Y.144, F.156, H.209, T.211, R.220, L.222 Ligands: NI.7, HY0.9 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:L.102, C:L.142, C:F.156 Hydrogen bonds: C:Y.92, C:Y.144, C:Y.144 Salt bridges: C:H.105, C:K.140, C:R.220 AKG.11: 14 residues within 4Å: Chain D: Y.92, L.94, L.102, H.105, K.140, L.142, Y.144, F.156, H.209, T.211, R.220, L.222 Ligands: NI.10, HY0.12 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:L.102, D:L.142, D:F.156 Hydrogen bonds: D:Y.144 Water bridges: D:R.96 Salt bridges: D:H.105, D:K.140, D:R.220

4 x HY0: HYGROMYCIN B VARIANT(Non-covalent)

HY0.3: 15 residues within 4Å: Chain A: F.49, R.54, E.90, Y.92, L.102, H.105, K.140, E.205, W.235, E.237, Y.250, D.252, V.255, E.257 Ligands: AKG.2 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:R.54, A:R.54, A:E.90, A:Y.138, A:K.140, A:E.205, A:E.237, A:D.252 Water bridges: A:P.47, A:E.90, A:Y.92, A:Y.92, A:S.124, A:E.205, A:D.252, A:D.252, A:D.252, A:D.252, A:V.255, A:E.257 HY0.6: 15 residues within 4Å: Chain B: F.49, R.54, E.90, Y.92, L.102, H.105, K.140, E.205, W.235, E.237, Y.250, D.252, V.255, E.257 Ligands: AKG.5 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:R.54, B:R.54, B:E.90, B:K.140, B:E.237, B:D.252, B:D.252 Water bridges: B:E.90, B:Y.92, B:S.124, B:E.205, B:D.252, B:D.252, B:H.253 HY0.9: 17 residues within 4Å: Chain C: F.49, R.54, E.90, Y.92, L.102, H.105, Y.138, K.140, E.205, W.235, E.237, Y.250, D.252, V.255, E.257 Ligands: NI.7, AKG.8 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:R.54, C:R.54, C:E.90, C:Y.138, C:K.140, C:E.205, C:E.237, C:D.252, C:E.257 Water bridges: C:S.124, C:D.252, C:D.258 HY0.12: 17 residues within 4Å: Chain D: F.49, R.54, E.90, Y.92, L.102, H.105, Y.138, K.140, E.205, W.235, E.237, Y.250, D.252, V.255, E.257 Ligands: NI.10, AKG.11 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:R.54, D:R.54, D:E.90, D:K.140, D:E.237, D:D.252, D:D.252, D:E.257 Water bridges: D:P.47, D:E.205, D:E.205, D:D.252, D:D.252, D:D.252, D:D.252, D:H.253

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McCulloch, K.M. et al., Oxidative cyclizations in orthosomycin biosynthesis expand the known chemistry of an oxygenase superfamily. Proc.Natl.Acad.Sci.USA (2015)

Release Date

2015-08-05

Peptides

oxidase/hydroxylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

oxidase/hydroxylase