SMTL ID : 1w3y.1

Crystal structure of S. pneumoniae hyaluronate lyase in complex with palmitoyl-vitamin C

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

1 x PVC: (2E,4R,5S)-2,3,4,5-TETRAHYDROXY-6-(PALMITOYLOXY)HEX-2-ENOIC ACID(Non-covalent)

PVC.1: 14 residues within 4Å: Chain A: N.123, W.124, W.125, R.169, F.176, E.221, H.232, T.233, Y.241, R.295, R.299, M.412, N.413 Ligands: XYL.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:W.124, A:F.176, A:H.232 Hydrogen bonds: A:N.123, A:W.125, A:Y.241, A:R.299, A:N.413 Water bridges: A:D.126, A:N.182, A:R.295, A:R.295 Salt bridges: A:H.232, A:R.295, A:R.295

2 x XYL: Xylitol(Non-covalent)

XYL.2: 5 residues within 4Å: Chain A: T.233, N.234, L.407, V.468 Ligands: PVC.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.233, A:N.234 XYL.3: 7 residues within 4Å: Chain A: Y.224, T.233, N.234, K.382, R.405, T.406, Q.711 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.218, A:T.233, A:K.382, A:R.405, A:Q.711

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

SO4.4: 5 residues within 4Å: Chain A: H.411, K.414, K.417, D.462, S.463 7 PLIP interactions: 7 interactions with chain A Water bridges: A:H.411, A:H.411, A:K.414, A:K.417, A:K.417 Salt bridges: A:H.411, A:K.417 SO4.5: 3 residues within 4Å: Chain A: A.461, D.462, S.463 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.462, A:S.463 Water bridges: A:S.463 SO4.6: 4 residues within 4Å: Chain A: Q.562, F.580, K.581, K.582 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.562, A:Q.562, A:K.582 Salt bridges: A:K.582 SO4.7: 1 residues within 4Å: Chain A: K.644 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.644 SO4.8: 3 residues within 4Å: Chain A: K.277, L.377, K.478 8 PLIP interactions: 8 interactions with chain A Water bridges: A:K.277, A:K.277, A:K.277, A:L.377, A:A.379, A:K.478 Salt bridges: A:K.277, A:K.478

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Botzki, A. et al., L-Ascorbic Acid 6-Hexadecanoate, a Potent Hyaluronidase Inhibitor: X-Ray Structure and Molecular Modeling of Enzyme-Inhibitor Complexes. J.Biol.Chem. (2004)

Release Date

2004-08-26

Peptides

HYALURONATE LYASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

HYALURONATE LYASE

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