SMTL ID : 1ur9.1

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 1.80 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: 21 residues within 4Å: Chain A: Y.10, F.12, F.51, G.96, W.97, Y.98, N.142, E.144, A.184, M.212, Y.214, D.215, Y.292, R.294, I.339, W.403, Q.407 Ligands: GOL.8, GOL.32, SO4.34, PHJ.40 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:N.142, A:N.142, A:Y.214, A:D.215, A:R.294, A:W.97, A:Y.98, A:Q.407 Water bridges: A:G.96 GDL-NAG.2: 20 residues within 4Å: Chain B: Y.10, F.12, F.51, G.96, W.97, Y.98, N.142, E.144, M.212, Y.214, D.215, Y.292, R.294, I.339, W.403, Q.407 Ligands: GOL.45, GOL.58, SO4.73, PHJ.77 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.10, B:W.403, B:Y.292, B:I.339 Hydrogen bonds: B:W.97, B:N.142, B:N.142, B:D.215, B:R.294, B:W.97, B:Y.98 Water bridges: B:G.96

64 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: R.244, T.256, F.259, P.260, S.261 Chain B: W.252 Ligand excluded by PLIP GOL.4: 4 residues within 4Å: Chain A: Y.481 Chain B: W.220 Ligands: GOL.45, PHJ.77 Ligand excluded by PLIP GOL.5: 10 residues within 4Å: Chain A: N.225, A.229, F.231, G.232, D.233, G.236, S.264, L.265, Y.307, T.363 Ligand excluded by PLIP GOL.6: 7 residues within 4Å: Chain A: T.3, R.4, K.5, A.6, T.45, H.46, Y.208 Ligand excluded by PLIP GOL.7: 8 residues within 4Å: Chain A: Y.145, A.186, G.187, G.188, F.191, M.212, Y.214 Ligands: PHJ.40 Ligand excluded by PLIP GOL.8: 8 residues within 4Å: Chain A: W.97, D.215, W.220, R.294 Ligands: GDL-NAG.1, GDL-NAG.1, SO4.34, PHJ.40 Ligand excluded by PLIP GOL.9: 6 residues within 4Å: Chain A: P.260, F.263, S.264, R.439, Y.440, T.441 Ligand excluded by PLIP GOL.10: 3 residues within 4Å: Chain A: T.37, P.38, A.39 Ligand excluded by PLIP GOL.11: 3 residues within 4Å: Chain A: G.298, S.311 Ligands: GOL.31 Ligand excluded by PLIP GOL.12: 2 residues within 4Å: Chain A: Q.350 Ligands: GOL.29 Ligand excluded by PLIP GOL.13: 3 residues within 4Å: Chain A: R.357, W.359, E.383 Ligand excluded by PLIP GOL.14: 3 residues within 4Å: Chain A: K.115, D.152 Ligands: GOL.28 Ligand excluded by PLIP GOL.15: 5 residues within 4Å: Chain A: Q.159, A.200, Q.201, A.204, P.205 Ligand excluded by PLIP GOL.16: 3 residues within 4Å: Chain A: Q.167, I.170, T.171 Ligand excluded by PLIP GOL.17: 5 residues within 4Å: Chain A: R.162, A.204, L.206, D.207, K.284 Ligand excluded by PLIP GOL.18: 4 residues within 4Å: Chain A: W.220, G.314 Ligands: PHJ.40, GOL.72 Ligand excluded by PLIP GOL.19: 5 residues within 4Å: Chain A: N.55, S.56, V.105, S.106, N.109 Ligand excluded by PLIP GOL.20: 4 residues within 4Å: Chain A: W.359, N.360, D.361, K.362 Ligand excluded by PLIP GOL.21: 4 residues within 4Å: Chain A: D.152, K.198, N.247 Ligands: SO4.38 Ligand excluded by PLIP GOL.22: 4 residues within 4Å: Chain A: R.89, L.177, P.178, Q.180 Ligand excluded by PLIP GOL.23: 6 residues within 4Å: Chain A: P.30, E.330, R.343, Q.344, Q.347 Ligands: SO4.36 Ligand excluded by PLIP GOL.24: 3 residues within 4Å: Chain A: K.132, Q.168, T.171 Ligand excluded by PLIP GOL.25: 3 residues within 4Å: Chain A: K.393, Y.421, D.429 Ligand excluded by PLIP GOL.26: 5 residues within 4Å: Chain A: Y.21, T.22, E.23, T.24, R.77 Ligand excluded by PLIP GOL.27: 10 residues within 4Å: Chain A: F.12, I.13, P.14, T.15, I.18, F.49, S.50, F.51, Y.99 Ligands: GOL.32 Ligand excluded by PLIP GOL.28: 7 residues within 4Å: Chain A: V.111, V.114, K.115, A.149, E.150, G.153 Ligands: GOL.14 Ligand excluded by PLIP GOL.29: 2 residues within 4Å: Chain A: Q.350 Ligands: GOL.12 Ligand excluded by PLIP GOL.30: 2 residues within 4Å: Chain A: P.237, T.238 Ligand excluded by PLIP GOL.31: 6 residues within 4Å: Chain A: K.297, W.324, V.326, N.373, L.375 Ligands: GOL.11 Ligand excluded by PLIP GOL.32: 7 residues within 4Å: Chain A: F.12, P.14, T.15, Y.98, Y.99 Ligands: GDL-NAG.1, GOL.27 Ligand excluded by PLIP GOL.39: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP GOL.41: 3 residues within 4Å: Chain B: P.281, S.282 Ligands: GOL.59 Ligand excluded by PLIP GOL.42: 10 residues within 4Å: Chain B: F.12, I.13, T.15, I.18, F.49, S.50, F.51, W.62, Y.99 Ligands: GOL.58 Ligand excluded by PLIP GOL.43: 9 residues within 4Å: Chain B: Y.145, A.186, G.187, G.188, F.191, M.212, Y.214, D.215 Ligands: PHJ.77 Ligand excluded by PLIP GOL.44: 2 residues within 4Å: Chain B: R.420, D.426 Ligand excluded by PLIP GOL.45: 8 residues within 4Å: Chain B: W.97, D.215, W.220, R.294 Ligands: GDL-NAG.2, GOL.4, SO4.73, PHJ.77 Ligand excluded by PLIP GOL.46: 3 residues within 4Å: Chain B: T.37, P.38, A.39 Ligand excluded by PLIP GOL.47: 4 residues within 4Å: Chain B: A.156, Q.159, E.160, T.163 Ligand excluded by PLIP GOL.48: 4 residues within 4Å: Chain B: K.390, Q.394, S.430, L.432 Ligand excluded by PLIP GOL.49: 5 residues within 4Å: Chain B: R.162, A.204, P.205, L.206, K.284 Ligand excluded by PLIP GOL.50: 4 residues within 4Å: Chain B: T.238, F.263, S.264, L.438 Ligand excluded by PLIP GOL.51: 5 residues within 4Å: Chain B: T.22, E.23, T.24, R.77 Ligands: GOL.76 Ligand excluded by PLIP GOL.52: 8 residues within 4Å: Chain B: D.53, I.54, N.55, A.61, W.62, D.63, P.64, Y.99 Ligand excluded by PLIP GOL.53: 2 residues within 4Å: Chain B: K.386, L.432 Ligand excluded by PLIP GOL.54: 3 residues within 4Å: Chain B: R.343, Q.347, R.410 Ligand excluded by PLIP GOL.55: 3 residues within 4Å: Chain B: T.24, D.25, T.26 Ligand excluded by PLIP GOL.56: 4 residues within 4Å: Chain B: R.89, L.177, P.178, Q.180 Ligand excluded by PLIP GOL.57: 5 residues within 4Å: Chain B: D.361, K.362, G.435, T.436, G.437 Ligand excluded by PLIP GOL.58: 6 residues within 4Å: Chain B: F.12, P.14, T.15, Y.98 Ligands: GDL-NAG.2, GOL.42 Ligand excluded by PLIP GOL.59: 5 residues within 4Å: Chain B: E.278, G.279, V.280, P.281 Ligands: GOL.41 Ligand excluded by PLIP GOL.60: 3 residues within 4Å: Chain B: V.223, P.237, T.238 Ligand excluded by PLIP GOL.61: 3 residues within 4Å: Chain B: R.77, A.80 Ligands: GOL.76 Ligand excluded by PLIP GOL.62: 4 residues within 4Å: Chain B: K.115, P.117, R.120 Ligands: GOL.64 Ligand excluded by PLIP GOL.63: 6 residues within 4Å: Chain A: A.148, A.149 Chain B: G.487, S.488, D.489 Ligands: SO4.38 Ligand excluded by PLIP GOL.64: 6 residues within 4Å: Chain B: V.114, K.115, R.120, D.152, G.153 Ligands: GOL.62 Ligand excluded by PLIP GOL.65: 5 residues within 4Å: Chain A: W.479, G.480, Y.481 Chain B: F.190, E.221 Ligand excluded by PLIP GOL.66: 3 residues within 4Å: Chain B: K.393, Y.421, F.422 Ligand excluded by PLIP GOL.67: 3 residues within 4Å: Chain B: K.42, D.419, N.423 Ligand excluded by PLIP GOL.68: 3 residues within 4Å: Chain B: D.152, K.198, N.247 Ligand excluded by PLIP GOL.69: 4 residues within 4Å: Chain A: W.252 Chain B: R.244, S.261, P.262 Ligand excluded by PLIP GOL.70: 5 residues within 4Å: Chain B: G.301, G.302, N.303, G.304, Y.369 Ligand excluded by PLIP GOL.71: 3 residues within 4Å: Chain B: R.129, K.132, D.133 Ligand excluded by PLIP GOL.72: 4 residues within 4Å: Chain A: W.220 Chain B: Y.481, I.482 Ligands: GOL.18 Ligand excluded by PLIP GOL.76: 2 residues within 4Å: Ligands: GOL.51, GOL.61 Ligand excluded by PLIP

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

SO4.33: 1 residues within 4Å: Chain A: R.420 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.420 Salt bridges: A:R.420 SO4.34: 5 residues within 4Å: Chain A: R.294, I.339 Ligands: GDL-NAG.1, GDL-NAG.1, GOL.8 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.338 Salt bridges: A:R.294 SO4.35: 2 residues within 4Å: Chain A: P.281, S.282 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.282 Water bridges: A:S.282, A:S.282, A:S.282, A:A.283, A:G.446 SO4.36: 5 residues within 4Å: Chain A: T.26, R.343, Q.347, R.410 Ligands: GOL.23 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.26 Water bridges: A:Q.347, A:Q.347, A:R.410 Salt bridges: A:R.410 SO4.37: 4 residues within 4Å: Chain A: P.14, N.16, Q.17, R.333 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.16, A:Q.17 Salt bridges: A:R.333 SO4.38: 6 residues within 4Å: Chain A: A.148, S.197, K.198, N.247 Ligands: GOL.21, GOL.63 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.197, A:N.247 Water bridges: A:S.197, A:N.247 Salt bridges: A:K.198 SO4.73: 5 residues within 4Å: Chain B: R.294, D.316 Ligands: GDL-NAG.2, GDL-NAG.2, GOL.45 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.294 SO4.74: 4 residues within 4Å: Chain B: P.14, N.16, Q.17, R.333 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.16, B:Q.17 Water bridges: B:R.333 Salt bridges: B:R.333 SO4.75: 2 residues within 4Å: Chain B: S.2, T.3 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.3, B:R.4

2 x PHJ: N-[(AMINOOXY)CARBONYL]-N-PHENYLAMINE(Non-covalent)

PHJ.40: 11 residues within 4Å: Chain A: W.97, E.144, Y.145, F.191, M.212, D.215, W.220 Ligands: GDL-NAG.1, GOL.7, GOL.8, GOL.18 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.97, A:F.191, A:D.215, A:W.220 Hydrogen bonds: A:E.144, A:Y.145, A:D.215 PHJ.77: 11 residues within 4Å: Chain B: W.97, E.144, Y.145, F.191, M.212, D.215, W.220 Ligands: GDL-NAG.2, GOL.4, GOL.43, GOL.45 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.97, B:F.191, B:D.215, B:W.220 Hydrogen bonds: B:E.144, B:D.215, B:D.215

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