SMTL ID : 1w1t.1

Crystal structure of S. marcescens chitinase B in complex with the cyclic dipeptide inhibitor cyclo-(His-L-Pro) at 1.9 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

19 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: F.190, E.221, F.239 Chain B: W.479, G.480, Y.481 Ligands: GOL.10 Ligand excluded by PLIP GOL.2: 6 residues within 4Å: Chain A: P.260, F.263, S.264, R.439, Y.440, T.441 Ligand excluded by PLIP GOL.3: 7 residues within 4Å: Chain A: T.3, R.4, T.45, H.46, S.87, R.89, Y.208 Ligand excluded by PLIP GOL.4: 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.5: 5 residues within 4Å: Chain A: R.162, A.204, L.206, D.207, K.284 Ligand excluded by PLIP GOL.6: 8 residues within 4Å: Chain A: F.190, F.191, S.193, R.194 Chain B: W.479, S.484, D.489, A.491 Ligand excluded by PLIP GOL.7: 2 residues within 4Å: Chain A: R.72, N.76 Ligand excluded by PLIP GOL.8: 8 residues within 4Å: Chain A: F.12, I.13, P.14, T.15, S.50, F.51, D.63, Y.99 Ligand excluded by PLIP GOL.9: 8 residues within 4Å: Chain A: D.215, Y.292, R.294, I.339, W.403, Q.407 Ligands: CHQ.14, CHQ.15 Ligand excluded by PLIP GOL.10: 9 residues within 4Å: Chain A: F.190, D.215, L.216, A.217, W.220, E.221, F.239 Ligands: GOL.1, CHQ.15 Ligand excluded by PLIP GOL.11: 7 residues within 4Å: Chain A: Y.323, L.325, V.326, G.327, C.328, E.329, V.332 Ligand excluded by PLIP GOL.16: 8 residues within 4Å: Chain A: W.479, G.480, Y.481, D.489 Chain B: F.190, F.191, R.194 Ligands: GOL.22 Ligand excluded by PLIP GOL.17: 6 residues within 4Å: Chain B: T.3, R.4, K.5, A.6, T.45 Ligands: GOL.20 Ligand excluded by PLIP GOL.18: 7 residues within 4Å: Chain B: Y.323, L.325, V.326, G.327, C.328, E.329, V.332 Ligand excluded by PLIP GOL.19: 6 residues within 4Å: Chain B: P.260, F.263, S.264, R.439, Y.440, T.441 Ligand excluded by PLIP GOL.20: 5 residues within 4Å: Chain B: R.89, L.177, P.178, Q.180 Ligands: GOL.17 Ligand excluded by PLIP GOL.21: 6 residues within 4Å: Chain B: R.162, A.204, P.205, L.206, D.207, K.284 Ligand excluded by PLIP GOL.22: 6 residues within 4Å: Chain A: W.479, G.480 Chain B: F.190, E.221, F.239 Ligands: GOL.16 Ligand excluded by PLIP GOL.23: 8 residues within 4Å: Chain B: D.215, Y.292, R.294, I.339, W.403, Q.407 Ligands: CHQ.28, CHQ.29 Ligand excluded by PLIP

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

SO4.12: 1 residues within 4Å: Chain A: R.420 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.420 SO4.13: 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 SO4.24: 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 SO4.25: 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 SO4.26: 2 residues within 4Å: Chain B: P.454, A.455 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.455 SO4.27: 3 residues within 4Å: Chain B: T.26, R.343, R.410 8 PLIP interactions: 8 interactions with chain B Water bridges: B:T.26, B:T.26, B:N.35, B:R.343, B:R.343, B:R.410 Salt bridges: B:R.343, B:R.410

4 x CHQ: CYCLO-(L-HISTIDINE-L-PROLINE) INHIBITOR(Non-covalent)

CHQ.14: 12 residues within 4Å: Chain A: Y.10, F.51, G.96, W.97, D.142, E.144, M.212, Y.214, D.215, W.403 Ligands: GOL.9, CHQ.15 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.10, A:F.51 Hydrogen bonds: A:W.97, A:Y.214, A:D.215 Water bridges: A:Y.98 CHQ.15: 7 residues within 4Å: Chain A: W.97, F.191, D.215, W.220 Ligands: GOL.9, GOL.10, CHQ.14 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.220 pi-Stacking: A:W.97 pi-Cation interactions: A:R.294 CHQ.28: 12 residues within 4Å: Chain B: Y.10, F.51, G.96, W.97, D.142, E.144, M.212, Y.214, D.215, W.403 Ligands: GOL.23, CHQ.29 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.10, B:F.51 Hydrogen bonds: B:W.97, B:D.215, B:D.215 Water bridges: B:Y.98 CHQ.29: 6 residues within 4Å: Chain B: W.97, F.191, D.215, W.220 Ligands: GOL.23, CHQ.28 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.191, B:W.220 Water bridges: B:R.294, B:R.294 pi-Stacking: B:W.97

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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