SMTL ID : 4ufq.2 (1 other biounit)

Structure of a novel Hyaluronidase (Hyal_Sk) from Streptomyces koganeiensis.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-trimer

Ligands

9 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 6 residues within 4Å: Chain A: S.64 Chain B: A.74, R.75, G.76, K.79 Chain C: S.97 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:G.76, A:S.64 Water bridges: B:R.75, B:K.79, B:K.79, A:Y.67, A:Y.67 Salt bridges: B:R.75, B:K.79 SO4.2: 5 residues within 4Å: Chain A: N.122, R.127, K.138, A.150 Chain C: Q.108 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.122 Water bridges: A:K.138, A:K.138, A:K.138, A:K.138 Salt bridges: A:R.127, A:K.138 SO4.3: 2 residues within 4Å: Chain A: D.148, R.162 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.148 Salt bridges: A:R.162 SO4.14: 6 residues within 4Å: Chain A: S.97 Chain B: S.64 Chain C: A.74, R.75, G.76, K.79 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:G.76, B:S.64 Water bridges: C:R.75, C:K.79, C:K.79, B:Y.67, B:Y.67 Salt bridges: C:R.75, C:K.79 SO4.15: 5 residues within 4Å: Chain A: Q.108 Chain B: N.122, R.127, K.138, A.150 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.122 Water bridges: B:K.138, B:K.138, B:K.138, B:K.138 Salt bridges: B:R.127, B:K.138 SO4.16: 2 residues within 4Å: Chain B: D.148, R.162 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.148 Salt bridges: B:R.162 SO4.27: 6 residues within 4Å: Chain A: A.74, R.75, G.76, K.79 Chain B: S.97 Chain C: S.64 9 PLIP interactions: 3 interactions with chain C, 6 interactions with chain A Hydrogen bonds: C:S.64, A:G.76 Water bridges: C:Y.67, C:Y.67, A:R.75, A:K.79, A:K.79 Salt bridges: A:R.75, A:K.79 SO4.28: 5 residues within 4Å: Chain B: Q.108 Chain C: N.122, R.127, K.138, A.150 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:N.122 Water bridges: C:K.138, C:K.138, C:K.138, C:K.138 Salt bridges: C:R.127, C:K.138 SO4.29: 2 residues within 4Å: Chain C: D.148, R.162 2 PLIP interactions: 2 interactions with chain C Water bridges: C:D.148 Salt bridges: C:R.162

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

NA.4: 4 residues within 4Å: Chain A: T.23, T.24, L.25 Chain C: E.17 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:E.17, A:T.24, A:T.24 NA.5: 3 residues within 4Å: Chain A: T.212, T.213, I.214 No protein-ligand interaction detected (PLIP) NA.6: 1 residues within 4Å: Chain A: T.47 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.47 Water bridges: A:T.47 NA.13: 1 residues within 4Å: Chain C: R.101 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.101, C:R.101 NA.17: 4 residues within 4Å: Chain A: E.17 Chain B: T.23, T.24, L.25 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.23, B:T.24, A:E.17 NA.18: 3 residues within 4Å: Chain B: T.212, T.213, I.214 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.213 NA.19: 1 residues within 4Å: Chain B: T.47 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.47 Water bridges: B:T.47, B:T.47 NA.26: 1 residues within 4Å: Chain A: R.101 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.101, A:R.101 NA.30: 4 residues within 4Å: Chain B: E.17 Chain C: T.23, T.24, L.25 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:T.23, C:T.24, B:E.17 NA.31: 3 residues within 4Å: Chain C: T.212, T.213, I.214 No protein-ligand interaction detected (PLIP) NA.32: 1 residues within 4Å: Chain C: T.47 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.47, C:T.47 Water bridges: C:T.47 NA.39: 1 residues within 4Å: Chain B: R.101 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.101, B:R.101

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 4 residues within 4Å: Chain A: F.29, K.31 Chain B: Y.43 Ligands: PEG.37 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain B: F.29, K.31 Chain C: Y.43 Ligands: PEG.11 Ligand excluded by PLIP CL.33: 4 residues within 4Å: Chain A: Y.43 Chain C: F.29, K.31 Ligands: PEG.24 Ligand excluded by PLIP

15 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 7 residues within 4Å: Chain A: R.142, T.152, P.153, R.154 Chain B: D.164, A.165, L.166 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.142, A:R.142 PEG.9: 7 residues within 4Å: Chain A: T.140, R.142, Q.156 Chain B: R.162, G.163, D.164, A.165 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.142, A:R.142, A:Q.156, A:Q.156, B:D.164 PEG.10: 3 residues within 4Å: Chain A: K.31, T.33 Chain C: D.22 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:D.22, A:K.31 PEG.11: 7 residues within 4Å: Chain A: N.55, I.57 Chain B: F.29 Chain C: H.38, T.41, Y.43 Ligands: CL.20 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:N.55, C:T.41 Water bridges: C:Y.43 PEG.12: 4 residues within 4Å: Chain A: A.150, A.151, T.152, R.154 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.152, A:T.152, A:R.154 PEG.21: 7 residues within 4Å: Chain B: R.142, T.152, P.153, R.154 Chain C: D.164, A.165, L.166 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.142, B:R.142 PEG.22: 7 residues within 4Å: Chain B: T.140, R.142, Q.156 Chain C: R.162, G.163, D.164, A.165 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:R.142, B:R.142, B:Q.156, B:Q.156, C:D.164 PEG.23: 3 residues within 4Å: Chain A: D.22 Chain B: K.31, T.33 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.31, A:D.22 PEG.24: 7 residues within 4Å: Chain A: H.38, T.41, Y.43 Chain B: N.55, I.57 Chain C: F.29 Ligands: CL.33 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.41, B:N.55 Water bridges: A:Y.43 PEG.25: 4 residues within 4Å: Chain B: A.150, A.151, T.152, R.154 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.152, B:T.152, B:R.154 PEG.34: 7 residues within 4Å: Chain A: D.164, A.165, L.166 Chain C: R.142, T.152, P.153, R.154 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.142, C:R.142 PEG.35: 7 residues within 4Å: Chain A: R.162, G.163, D.164, A.165 Chain C: T.140, R.142, Q.156 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:R.142, C:R.142, C:Q.156, C:Q.156, A:D.164 PEG.36: 3 residues within 4Å: Chain B: D.22 Chain C: K.31, T.33 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:K.31, B:D.22 PEG.37: 7 residues within 4Å: Chain A: F.29 Chain B: H.38, T.41, Y.43 Chain C: N.55, I.57 Ligands: CL.7 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:N.55, B:T.41 Water bridges: B:Y.43 PEG.38: 4 residues within 4Å: Chain C: A.150, A.151, T.152, R.154 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.152, C:T.152, C:R.154

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Messina, L. et al., Identification and Characterization of a Bacterial Hyaluronidase and its Production in Recombinant Form. FEBS Lett. (2016)

Release Date

2016-04-13

Peptides

Hyaluronidase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Hyaluronidase

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