SMTL ID : 6x3m.2 (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- 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.1: 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 Ligands: NAG-BDP-NAG-GCD.5 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Salt bridges: B:R.196 Hydrogen bonds: A:S.162, B:R.196, B:R.196 NAG-BDP-NAG-BDP-NAG-BDP-NAG-GCD.3: 20 residues within 4Å: Chain A: R.196, F.230, N.235, I.236, 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, I.248, R.249 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:S.160, C:S.162, A:R.196 Salt bridges: A:R.196 NAG-BDP-NAG-BDP-NAG-BDP-NAG-GCD.4: 19 residues within 4Å: Chain A: T.215, N.216, N.219, R.223, K.259, T.261 Chain B: S.160, S.161, S.162, F.208, Q.247, I.248, R.249 Chain C: P.191, R.196, F.230, N.235, T.237 Ligands: NAG-BDP-NAG-GCD.2 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.196 Hydrogen bonds: C:R.196

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.2: 12 residues within 4Å: Chain A: A.254, L.255, G.256, K.259, R.311, R.313 Chain B: Q.295, Y.298 Chain C: E.273, N.274, A.276 Ligands: NAG-BDP-NAG-BDP-NAG-BDP-NAG-GCD.4 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: B:Q.295, B:Q.295, A:R.313, A:R.313, C:N.274, C:A.276, A:L.255 Salt bridges: A:R.313, A:K.259 NAG-BDP-NAG-GCD.5: 12 residues within 4Å: Chain A: Q.295, Y.298 Chain B: E.273, N.274 Chain C: A.254, L.255, K.259, K.308, R.311, R.313, D.318 Ligands: NAG-BDP-NAG-BDP-NAG-BDP-NAG-GCD.1 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: A:Q.295, A:Y.298, B:D.281, C:A.254 Salt bridges: C:K.259 NAG-BDP-NAG-GCD.6: 9 residues within 4Å: Chain A: N.274, S.279 Chain B: A.254, L.255, K.259, R.311, R.313 Chain C: Q.295, Y.298 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.279, B:K.259, B:K.259

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
D

B
E

C
F

Hyaluronoglucosaminidase

Related Entries With Identical Sequence