SMTL ID : 1o6i.1

Chitinase B from Serratia marcescens complexed with the catalytic intermediate mimic cyclic dipeptide CI4.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x 0HZ: amino({3-[(3S,8aS)-1,4-dioxooctahydropyrrolo[1,2-a]pyrazin-3-yl]propyl}amino)methaniminium(Non-covalent)

0HZ.1: 12 residues within 4Å: Chain A: Y.10, F.12, F.51, G.96, W.97, D.142, E.144, A.184, M.212, Y.214, W.403 Ligands: GOL.15 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.10, A:A.184, A:W.403 Hydrogen bonds: A:W.97, A:Y.214 Water bridges: A:Y.98, A:H.404 0HZ.21: 12 residues within 4Å: Chain B: Y.10, F.51, G.96, W.97, D.142, E.144, A.184, M.212, Y.214, W.403 Ligands: GOL.33, GOL.36 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.184, B:W.403 Hydrogen bonds: B:W.97 Water bridges: B:Y.98, B:Y.98, B:D.215

31 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: W.220 Chain B: Y.481 Ligands: GOL.16, GOL.22 Ligand excluded by PLIP GOL.3: 10 residues within 4Å: Chain A: W.479, G.480, Y.481, I.482, D.489, A.491 Chain B: F.190, F.191, R.194 Ligands: GOL.20 Ligand excluded by PLIP GOL.4: 6 residues within 4Å: Chain A: P.260, F.263, S.264, R.439, Y.440, T.441 Ligand excluded by PLIP GOL.5: 6 residues within 4Å: Chain A: T.3, R.4, T.45, H.46, R.89, Y.208 Ligand excluded by PLIP GOL.6: 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.7: 5 residues within 4Å: Chain A: R.162, A.204, L.206, D.207, K.284 Ligand excluded by PLIP GOL.8: 4 residues within 4Å: Chain A: S.300, Y.307, S.308, S.309 Ligand excluded by PLIP GOL.9: 3 residues within 4Å: Chain A: K.132, Q.168, T.171 Ligand excluded by PLIP GOL.10: 9 residues within 4Å: Chain A: F.190, F.191, S.193, R.194 Chain B: W.479, Y.481, S.484, D.489, A.491 Ligand excluded by PLIP GOL.11: 2 residues within 4Å: Chain A: R.72, N.76 Ligand excluded by PLIP GOL.12: 5 residues within 4Å: Chain A: S.197, L.248, W.250, M.277, E.278 Ligand excluded by PLIP GOL.13: 4 residues within 4Å: Chain A: F.231, Q.394, M.434, R.439 Ligand excluded by PLIP GOL.14: 7 residues within 4Å: Chain A: A.246, N.247, L.248, G.249 Chain B: G.249, W.250, S.251 Ligand excluded by PLIP GOL.15: 6 residues within 4Å: Chain A: Y.292, R.294, I.339, W.403, Q.407 Ligands: 0HZ.1 Ligand excluded by PLIP GOL.16: 8 residues within 4Å: Chain A: F.190, D.215, L.216, W.220, E.221, L.265 Ligands: GOL.2, GOL.22 Ligand excluded by PLIP GOL.20: 9 residues within 4Å: Chain A: W.479, G.480, Y.481 Chain B: F.190, E.221, F.239 Ligands: GOL.3, GOL.31, GOL.34 Ligand excluded by PLIP GOL.22: 7 residues within 4Å: Chain A: E.221, F.239 Chain B: W.479, G.480, Y.481 Ligands: GOL.2, GOL.16 Ligand excluded by PLIP GOL.23: 7 residues within 4Å: Chain B: T.3, R.4, T.45, H.46, R.89, Y.208 Ligands: GOL.26 Ligand excluded by PLIP GOL.24: 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.25: 6 residues within 4Å: Chain B: P.260, F.263, S.264, R.439, Y.440, T.441 Ligand excluded by PLIP GOL.26: 5 residues within 4Å: Chain B: R.89, L.177, P.178, Q.180 Ligands: GOL.23 Ligand excluded by PLIP GOL.27: 3 residues within 4Å: Chain B: T.26, R.343, R.410 Ligand excluded by PLIP GOL.28: 6 residues within 4Å: Chain B: R.162, A.204, P.205, L.206, D.207, K.284 Ligand excluded by PLIP GOL.29: 4 residues within 4Å: Chain B: R.4, K.42, Q.43, D.419 Ligand excluded by PLIP GOL.30: 2 residues within 4Å: Chain B: N.16, N.19 Ligand excluded by PLIP GOL.31: 6 residues within 4Å: Chain B: G.187, G.188, F.190, F.191 Ligands: GOL.20, GOL.34 Ligand excluded by PLIP GOL.32: 2 residues within 4Å: Chain B: E.383, K.386 Ligand excluded by PLIP GOL.33: 4 residues within 4Å: Chain B: W.97, F.191 Ligands: 0HZ.21, GOL.34 Ligand excluded by PLIP GOL.34: 5 residues within 4Å: Chain A: Y.481 Chain B: W.220 Ligands: GOL.20, GOL.31, GOL.33 Ligand excluded by PLIP GOL.35: 4 residues within 4Å: Chain B: K.390, K.393, D.429, S.430 Ligand excluded by PLIP GOL.36: 6 residues within 4Å: Chain B: Y.292, R.294, W.403, H.404, Q.407 Ligands: 0HZ.21 Ligand excluded by PLIP

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

SO4.17: 2 residues within 4Å: Chain A: Y.470, Q.471 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.471 SO4.18: 1 residues within 4Å: Chain A: R.420 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.420 SO4.19: 2 residues within 4Å: Chain A: P.281, S.282 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.282 Water bridges: A:S.282, A:S.282, A:S.282, A:S.282, A:S.282, A:A.283 SO4.37: 1 residues within 4Å: Chain B: R.420 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.420 SO4.38: 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 SO4.39: 2 residues within 4Å: Chain B: P.454, A.455 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.455 Water bridges: B:A.453

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Houston, D.R. et al., The cyclic dipeptide CI-4 [cyclo-(l-Arg-d-Pro)] inhibits family 18 chitinases by structural mimicry of a reaction intermediate. Biochem. J. (2002)

Release Date

2003-03-30

Peptides

Chitinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Chitinase

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