SMTL ID : 6x3m.3 (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: 11 residues within 4Å: Chain A: E.273, N.274, A.276 Chain B: A.254, L.255, G.256, K.259, R.311, R.313 Chain C: Q.295, Y.298 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: C:Q.295, A:E.273, B:R.311, B:R.313, B:A.254, A:N.274, B:R.313 Salt bridges: B:R.313, B:K.259 NAG-BDP-NAG-GCD.5: 10 residues within 4Å: Chain A: Q.295, Y.298 Chain B: E.273, N.274, D.281 Chain C: A.254, L.255, K.259, R.311, R.313 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: B:E.273, B:N.274, C:R.313, C:K.259, C:A.254, B:N.274, A:Y.298 Salt bridges: C:R.313 NAG-BDP-NAG-GCD.6: 11 residues within 4Å: Chain A: A.254, L.255, K.259, R.311, R.313 Chain B: Q.295, Y.298, T.302 Chain C: N.274, D.281 Ligands: NAG-BDP-NAG-BDP-NAG-BDP-NAG-GCD.2 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: A:R.313, A:R.313, B:Q.295, C:N.274 Salt bridges: A:R.311, A:R.313, A:K.259 Hydrophobic interactions: B: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: 18 residues within 4Å: Chain A: N.216, N.219, V.221, R.223, K.259, T.261 Chain B: P.159, S.160, S.161, S.162, F.208, Q.247, R.249 Chain C: R.196, F.230, N.235, T.237 Ligands: NAG-BDP-NAG-GCD.6 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:S.161, B:S.162, B:S.162, B:S.162, C:R.196, C:R.196, C:R.196 NAG-BDP-NAG-BDP-NAG-BDP-NAG-GCD.3: 20 residues within 4Å: Chain A: 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, F.208, Q.247, I.248, R.249 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:S.160, C:S.161, A:R.196 NAG-BDP-NAG-BDP-NAG-BDP-NAG-GCD.4: 18 residues within 4Å: Chain A: P.159, S.160, S.161, S.162, Q.204, S.205, F.208, Q.247, R.249 Chain B: F.230, T.237 Chain C: T.215, N.216, N.219, V.221, R.223, K.259, T.261 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.161, A:S.162, A:S.162

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
G

B
H

C
I

Hyaluronoglucosaminidase

Related Entries With Identical Sequence