SMTL ID : 6wxa.1

Crystal structure of truncated Streptococcal bacteriophage hyaluronidase complexed with unsaturated hyaluronan hexa-saccharides

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-trimer

Ligands

2 x 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

NAG-BDP-NAG-BDP-NAG-GCD.1: 22 residues within 4Å: Chain A: P.73, S.74, S.75, F.122, Q.161, I.162, R.163 Chain B: G.104, P.105, I.108, R.110, F.144, N.149, T.151 Chain C: T.129, N.130, N.133, V.135, R.137, K.173, T.175 Ligands: NAG-BDP-NAG-GCD.5 6 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A, 2 interactions with chain B Water bridges: C:R.137, C:R.137, B:R.110 Salt bridges: C:R.137, B:R.110 Hydrogen bonds: A:S.75, A:S.76, A:S.75 NAG-BDP-NAG-BDP-NAG-GCD.4: 22 residues within 4Å: Chain A: G.104, P.105, I.108, R.110, F.144, N.149, T.151 Chain B: T.129, N.130, N.133, V.135, R.137, K.173, T.175 Chain C: P.73, S.74, S.75, S.76, F.122, Q.161, I.162, R.163 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C Salt bridges: B:R.137, A:R.110 Hydrogen bonds: C:S.75, C:S.76, C:S.75

1 x NAG- BDP- NAG- BDP- NAG: 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.2: 19 residues within 4Å: Chain A: T.129, N.130, N.133, V.135, R.137, K.173, T.175 Chain B: P.73, S.74, S.75, F.122, Q.161, I.162, R.163 Chain C: P.105, I.108, F.144, N.149, T.151 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Water bridges: A:N.133, A:N.133, A:R.137, B:Q.118, B:S.119 Salt bridges: A:R.137 Hydrogen bonds: B:P.73, B:S.75

2 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.3: 13 residues within 4Å: Chain A: E.187, N.188, A.189, A.190, S.193 Chain B: A.168, L.169, G.170, K.173, R.225, R.227 Chain C: Q.209, Y.212 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: B:R.227, B:R.227, C:Q.209, C:Q.209, A:N.188, A:S.193, B:L.169 Salt bridges: B:R.227, B:K.173 NAG-BDP-NAG-GCD.5: 14 residues within 4Å: Chain A: Q.209, Y.212 Chain B: E.187, N.188, A.189, A.190, S.193 Chain C: A.168, L.169, G.170, K.173, R.225, R.227 Ligands: NAG-BDP-NAG-BDP-NAG-GCD.1 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: C:R.225, C:R.225, C:R.227, C:R.227, A:Q.209, A:Q.209, C:L.169, B:N.188, B:S.193 Salt bridges: C:R.227, C:K.173 Water bridges: B:S.193

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

NI.6: 6 residues within 4Å: Chain A: H.289, H.291 Chain B: H.289, H.291 Chain C: H.289, H.291 6 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A, 2 interactions with chain C Metal complexes: B:H.289, B:H.291, A:H.289, A:H.291, C:H.289, C:H.291

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

2021-05-12

Peptides

Hyaluronan lyase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Hyaluronan lyase

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