SMTL ID : 1ur8.1

Interactions of a family 18 chitinase with the designed inhibitor HM508, and its degradation product, chitobiono-delta-lactone

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x GDL- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-(acetylamido)-2-deoxy-D-glucono-1,5-lactone(Non-covalent)

GDL-NAG.1: 17 residues within 4Å: Chain A: Y.10, F.12, F.51, G.96, W.97, Y.98, D.142, E.144, A.184, M.212, Y.214, D.215, Y.292, R.294, I.339, W.403, Q.407 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.10, A:A.184, A:W.403, A:Y.292, A:I.339 Hydrogen bonds: A:W.97, A:D.142, A:Y.214, A:D.215, A:R.294, A:Y.98, A:Q.407 Water bridges: A:G.96, A:R.294 GDL-NAG.2: 17 residues within 4Å: Chain B: Y.10, F.12, F.51, G.96, W.97, Y.98, D.142, E.144, M.212, Y.214, D.215, Y.292, R.294, I.339, W.403, Q.407 Ligands: SO4.18 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.10, B:W.403, B:Y.292, B:I.339 Hydrogen bonds: B:W.97, B:D.142, B:D.215, B:R.294, B:W.97, B:Y.98, B:Q.407 Water bridges: B:G.96

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: P.260, F.263, S.264, R.439, Y.440, T.441 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.264, A:S.264, A:T.441, A:T.441 Water bridges: A:S.264 GOL.4: 4 residues within 4Å: Chain A: N.55, S.56, P.64, N.109 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.56 Water bridges: A:N.109 GOL.5: 3 residues within 4Å: Chain A: R.343, Q.347, R.410 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.343, A:Q.347, A:R.410 Water bridges: A:R.343, A:R.410 GOL.9: 5 residues within 4Å: Chain B: P.260, F.263, S.264, Y.440, T.441 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.264, B:S.264, B:T.441 GOL.10: 7 residues within 4Å: Chain B: Y.323, L.325, V.326, G.327, C.328, E.329, V.332 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.323, B:G.327 GOL.11: 9 residues within 4Å: Chain A: F.190, S.193, R.194 Chain B: W.479, I.482, T.483, S.484, D.489, A.491 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:S.193, A:R.194, B:T.483, B:S.484, B:S.484, B:D.489 GOL.12: 6 residues within 4Å: Chain B: R.162, A.204, P.205, L.206, D.207, K.284 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.162, B:K.284 Water bridges: B:R.162, B:R.162, B:Q.180, B:A.204, B:D.207, B:K.284 GOL.13: 7 residues within 4Å: Chain A: W.479, G.480, Y.481, I.482 Chain B: F.190, F.191, R.194 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:F.190, B:R.194 Water bridges: A:G.480, A:G.480, A:G.480, A:D.489 GOL.14: 2 residues within 4Å: Chain B: P.454, A.455 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.455 Water bridges: B:S.469, B:S.469

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

SO4.6: 1 residues within 4Å: Chain A: R.420 6 PLIP interactions: 6 interactions with chain A Water bridges: A:R.420, A:D.426, A:D.426, A:D.426, A:D.426 Salt bridges: A:R.420 SO4.7: 5 residues within 4Å: Chain A: P.14, N.16, Q.17, V.28, R.333 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.333 SO4.8: 2 residues within 4Å: Chain A: P.281, S.282 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.282 Water bridges: A:S.282, A:S.282, A:A.283 SO4.15: 1 residues within 4Å: Chain B: R.420 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.420, B:R.420, B:D.426 Salt bridges: B:R.420 SO4.16: 2 residues within 4Å: Chain B: P.281, S.282 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.282 Water bridges: B:S.282, B:S.282, B:A.283 SO4.17: 5 residues within 4Å: Chain B: P.14, N.16, Q.17, V.28, R.333 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.16, B:Q.17, B:Q.17 Water bridges: B:R.333, B:R.333 Salt bridges: B:R.333 SO4.18: 3 residues within 4Å: Chain B: R.294 Ligands: GDL-NAG.2, GDL-NAG.2 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.294

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vaaje-Kolstad, G. et al., Interactions of a Family 18 Chitinase with the Designed Inhibitor Hm508 and its Degradation Product, Chitobiono-Delta-Lactone. J.Biol.Chem. (2004)

Release Date

2004-04-27

Peptides

CHITINASE B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

CHITINASE B

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