SMTL ID : 1w1y.1

CRYSTAL STRUCTURE OF S. MARCESCENS CHITINASE B IN COMPLEX WITH THE CYCLIC DIPEPTIDE INHIBITOR CYCLO-(L-TYR-L-PRO) AT 1.85 A RESOLUTION

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: D.215, L.216, A.217, W.220, E.221, F.239, L.265 Ligands: GOL.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.221, A:E.221 Water bridges: A:F.190 GOL.2: 10 residues within 4Å: Chain A: W.479, Y.481, I.482, T.483, D.489, A.491 Chain B: Q.147, F.190, F.191, R.194 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:R.194, A:Y.481, A:T.483, A:S.484 Water bridges: A:D.489, A:S.490 GOL.3: 6 residues within 4Å: Chain A: P.260, F.263, S.264, R.439, Y.440, T.441 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.264, A:S.264, A:T.441, A:T.441, A:G.442 Water bridges: A:R.439 GOL.4: 6 residues within 4Å: Chain A: R.244, T.256, F.259, P.260, S.261 Chain B: W.252 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.244, A:F.259, A:S.261 GOL.5: 5 residues within 4Å: Chain A: R.162, A.204, L.206, D.207, K.284 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.284 Water bridges: A:R.162, A:N.166, A:D.207, A:D.207, A:D.207 GOL.6: 7 residues within 4Å: Chain A: F.190, E.221, F.239 Chain B: W.479, G.480, Y.481 Ligands: GOL.1 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.480 GOL.12: 5 residues within 4Å: Chain B: T.3, R.4, T.45, H.46, R.89 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:R.4, B:H.46, B:R.89, B:Y.208 Water bridges: B:R.4, B:R.4, B:R.4, B:R.4, B:Q.180 GOL.13: 6 residues within 4Å: Chain B: P.260, F.263, S.264, R.439, Y.440, T.441 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.264, B:S.264, B:T.441, B:T.441 GOL.14: 10 residues within 4Å: Chain A: F.190, F.191, R.194 Chain B: W.479, Y.481, I.482, T.483, S.484, D.489, A.491 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:R.194, B:Y.481, B:T.483, B:S.484, B:D.489 Water bridges: A:F.190, B:A.491 GOL.15: 7 residues within 4Å: Chain A: W.479, G.480, Y.481 Chain B: F.190, E.221, F.239 Ligands: GOL.16 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.480 Water bridges: B:E.221 GOL.16: 8 residues within 4Å: Chain B: F.190, D.215, L.216, A.217, W.220, E.221, L.265 Ligands: GOL.15 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.215 Water bridges: B:G.188, B:F.190, B:D.215, B:W.220 GOL.17: 6 residues within 4Å: Chain A: W.252 Chain B: R.244, T.256, F.259, P.260, S.261 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.244, B:S.261, B:S.261

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

SO4.7: 2 residues within 4Å: Chain A: R.420, D.426 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.420 SO4.8: 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:S.282, A:A.283

7 x TYP: CYCLO-(L-TYROSINE-L-PROLINE) INHIBITOR(Non-covalent)

TYP.9: 17 residues within 4Å: Chain A: Y.10, 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 Ligands: TYP.10, TYP.11 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.10, A:Y.10, A:F.51, A:Y.98, A:A.184, A:I.339 Hydrogen bonds: A:W.97, A:Y.98, A:Y.214 Water bridges: A:E.144, A:R.294 pi-Cation interactions: A:R.294 TYP.10: 9 residues within 4Å: Chain A: F.12, F.51, G.96, W.97, Y.98, D.334, D.336, W.403 Ligands: TYP.9 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.51, A:D.336, A:W.403 Hydrogen bonds: A:Y.98 Water bridges: A:G.96, A:Q.407, A:Q.407 pi-Stacking: A:F.12, A:Y.98 TYP.11: 8 residues within 4Å: Chain A: W.97, L.103, F.191, D.215, W.220 Chain B: Y.481, T.483 Ligands: TYP.9 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:W.97, A:W.97, A:W.220, B:Y.481, B:Y.481 Water bridges: B:T.483 TYP.18: 16 residues within 4Å: Chain B: Y.10, F.51, G.96, W.97, Y.98, D.142, E.144, A.184, M.212, Y.214, D.215, Y.292, R.294, W.403 Ligands: TYP.19, TYP.20 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Y.10, B:Y.10, B:F.51, B:Y.98, B:A.184 Hydrogen bonds: B:W.97, B:Y.98, B:Y.98, B:Y.292 Water bridges: B:E.144, B:R.294 pi-Cation interactions: B:R.294 TYP.19: 9 residues within 4Å: Chain B: F.12, F.51, G.96, W.97, Y.98, D.334, D.336, W.403 Ligands: TYP.18 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.51, B:D.336, B:W.403 Hydrogen bonds: B:Y.98 Water bridges: B:Q.407, B:Q.407 pi-Stacking: B:F.12, B:Y.98 TYP.20: 8 residues within 4Å: Chain A: Y.481, T.483 Chain B: W.97, L.103, F.191, D.215, W.220 Ligands: TYP.18 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:Y.481, A:Y.481, A:Y.481, B:W.97, B:W.97, B:W.220 Water bridges: A:T.483, B:D.316 TYP.21: 10 residues within 4Å: Chain B: R.162, N.166, T.169, Q.175, P.178, A.204, P.205, L.206, D.207, K.284 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:P.178 Hydrogen bonds: B:R.162, B:N.166 Water bridges: B:R.162, B:Q.175, B:Q.175

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Houston, D.R. et al., Structure-Based Exploration of Cyclic Dipeptide Chitinase Inhibitors. J.Med.Chem. (2004)

Release Date

2005-01-10

Peptides

CHITINASE B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

CHITINASE B

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