SMTL ID : 6x3m.1 (2 other biounits)

Crystal structure of full-length Streptococcal bacteriophage hyaluronidase in complex with unsaturated hyaluronan octa-saccharides

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.58 Å

Oligo State

homo-trimer

Ligands

3 x NAG- BDP- NAG- GCD: 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-BDP-NAG-GCD.1: 13 residues within 4Å: Chain A: A.254, L.255, G.256, K.259, K.308, R.311, R.313 Chain B: Q.295, Y.298 Chain C: N.274, A.275, A.276 Ligands: NAG-BDP-NAG-BDP-NAG-BDP-NAG-GCD.3 6 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: A:R.313, A:R.313, B:Q.295, B:Q.295, C:N.274, C:A.276, A:L.255, A:L.255 Salt bridges: A:R.313, A:K.259 NAG-BDP-NAG-GCD.5: 7 residues within 4Å: Chain A: N.274 Chain B: A.254, G.256, R.311, R.313 Chain C: Q.295, Y.298 7 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A, 3 interactions with chain C Hydrogen bonds: B:R.311, B:R.311, B:R.313, B:R.313, A:N.274, B:A.254, B:G.256, B:G.256, C:Q.295, C:Y.298 Salt bridges: B:R.311 Hydrophobic interactions: C:Y.298 NAG-BDP-NAG-GCD.6: 9 residues within 4Å: Chain A: Q.295, Y.298 Chain B: N.274, S.279 Chain C: A.254, L.255, G.256, R.311, R.313 6 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: C:R.311, C:R.311, C:R.313, C:R.313, A:Q.295, A:Q.295, A:Y.298, C:L.255, C:G.256, B:N.274, B:S.279 Salt bridges: C:R.313, C:K.259 Hydrophobic interactions: A:Y.298

3 x NAG- BDP- NAG- BDP- NAG- BDP- NAG- GCD: 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-BDP-NAG-BDP-NAG-BDP-NAG-GCD.2: 21 residues within 4Å: Chain A: P.159, S.160, S.161, S.162, Q.204, F.208, Q.247, I.248, R.249 Chain B: P.191, I.194, R.196, F.230, N.235, T.237 Chain C: N.216, N.219, V.221, R.223, K.259, T.261 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.162 Salt bridges: B:R.196 NAG-BDP-NAG-BDP-NAG-BDP-NAG-GCD.3: 21 residues within 4Å: Chain A: N.219, V.221, R.223, K.259, T.261 Chain B: P.159, S.160, S.161, S.162, F.208, Q.247, I.248, R.249 Chain C: D.189, P.191, I.194, R.196, F.230, N.235, T.237 Ligands: NAG-BDP-NAG-GCD.1 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:S.161 Salt bridges: C:R.196 NAG-BDP-NAG-BDP-NAG-BDP-NAG-GCD.4: 21 residues within 4Å: Chain A: D.189, G.190, P.191, R.196, F.230, N.235, T.237 Chain B: T.215, N.216, N.219, V.221, R.223, K.259, T.261 Chain C: P.159, S.160, S.161, S.162, F.208, Q.247, R.249 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:S.162, C:S.162 Salt bridges: A:R.196

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, J.H. et al., Crystal Structure of Streptococcal Bacteriophage Hyaluronidase: Presence of a Prokaryotic Collagen and Elucidation of Catalytic Mechanism. To Be Published

Release Date

2021-06-09

Peptides

Hyaluronoglucosaminidase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Hyaluronoglucosaminidase

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