SMTL ID : 3wd4.2 (1 other biounit)

Serratia marcescens Chitinase B complexed with azide inhibitor and quinoline compound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

18 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: T.7, R.8, T.49, H.50, S.91, R.93, Y.212 Ligand excluded by PLIP GOL.2: 6 residues within 4Å: Chain A: P.264, F.267, S.268, R.443, Y.444, T.445 Ligand excluded by PLIP GOL.3: 6 residues within 4Å: Chain A: R.248, T.260, F.263, P.264, S.265 Chain B: W.256 Ligand excluded by PLIP GOL.4: 7 residues within 4Å: Chain A: Y.327, L.329, V.330, G.331, C.332, D.333, V.336 Ligand excluded by PLIP GOL.5: 6 residues within 4Å: Chain A: R.166, A.208, P.209, L.210, D.211, K.288 Ligand excluded by PLIP GOL.6: 6 residues within 4Å: Chain A: K.397, Y.425, Y.431, D.432, D.433, S.434 Ligand excluded by PLIP GOL.7: 4 residues within 4Å: Chain A: W.363, N.364, D.365, K.366 Ligand excluded by PLIP GOL.8: 4 residues within 4Å: Chain A: A.467, Q.468, G.484, Y.485 Ligand excluded by PLIP GOL.9: 6 residues within 4Å: Chain A: F.235, Y.395, Q.398, Q.399, M.438, R.443 Ligand excluded by PLIP GOL.13: 7 residues within 4Å: Chain B: T.7, R.8, T.49, H.50, S.91, R.93, Y.212 Ligand excluded by PLIP GOL.14: 6 residues within 4Å: Chain B: P.264, F.267, S.268, R.443, Y.444, T.445 Ligand excluded by PLIP GOL.15: 6 residues within 4Å: Chain A: W.256 Chain B: R.248, T.260, F.263, P.264, S.265 Ligand excluded by PLIP GOL.16: 7 residues within 4Å: Chain B: Y.327, L.329, V.330, G.331, C.332, D.333, V.336 Ligand excluded by PLIP GOL.17: 6 residues within 4Å: Chain B: R.166, A.208, P.209, L.210, D.211, K.288 Ligand excluded by PLIP GOL.18: 6 residues within 4Å: Chain B: K.397, Y.425, Y.431, D.432, D.433, S.434 Ligand excluded by PLIP GOL.19: 4 residues within 4Å: Chain B: W.363, N.364, D.365, K.366 Ligand excluded by PLIP GOL.20: 4 residues within 4Å: Chain B: A.467, Q.468, G.484, Y.485 Ligand excluded by PLIP GOL.21: 6 residues within 4Å: Chain B: F.235, Y.395, Q.398, Q.399, M.438, R.443 Ligand excluded by PLIP

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

SO4.10: 3 residues within 4Å: Chain A: K.390, R.424, Y.431 8 PLIP interactions: 8 interactions with chain A Water bridges: A:K.390, A:K.390, A:K.390, A:K.390, A:Y.425, A:Y.431 Salt bridges: A:K.390, A:R.424 SO4.22: 3 residues within 4Å: Chain B: K.390, R.424, Y.431 6 PLIP interactions: 6 interactions with chain B Water bridges: B:K.390, B:K.390, B:K.390, B:K.390 Salt bridges: B:K.390, B:R.424

2 x A1L: [2-[[(2S)-1-[bis(phenylmethyl)amino]-5-[[N-(methylcarbamoyl)carbamimidoyl]amino]-1-oxidanylidene-pentan-2-yl]amino]-2-oxidanylidene-ethyl]-diazonio-azanide(Non-covalent)

A1L.11: 15 residues within 4Å: Chain A: Y.14, F.16, F.55, W.101, D.146, E.148, M.216, Y.218, D.219, P.223, Y.296, R.298, R.342, W.407 Ligands: QUB.12 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:F.55, A:W.101, A:Y.296, A:Y.296, A:W.407 Hydrogen bonds: A:D.146, A:R.298, A:R.298 Water bridges: A:W.101, A:W.101, A:D.219, A:D.219, A:D.219, A:Y.296, A:E.319, A:R.342 Salt bridges: A:D.146, A:E.148, A:D.219 pi-Stacking: A:F.16 A1L.23: 15 residues within 4Å: Chain B: Y.14, F.16, F.55, W.101, D.146, E.148, M.216, Y.218, D.219, P.223, Y.296, R.298, R.342, W.407 Ligands: QUB.24 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:F.55, B:W.101, B:Y.296, B:Y.296, B:W.407 Hydrogen bonds: B:D.146, B:Y.218, B:R.298, B:R.298 Water bridges: B:W.101, B:W.101, B:Y.149, B:D.219, B:E.319, B:R.342 Salt bridges: B:D.146, B:E.148, B:D.219 pi-Stacking: B:F.16

2 x QUB: (E)-N-(prop-2-en-1-yloxy)-1-(quinolin-4-yl)methanimine(Non-covalent)

QUB.12: 7 residues within 4Å: Chain A: F.195, D.219, P.223, W.224, G.318, R.342 Ligands: A1L.11 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.195, A:D.219, A:P.223, A:W.224 pi-Stacking: A:W.224, A:W.224, A:W.224 QUB.24: 7 residues within 4Å: Chain B: F.195, D.219, P.223, W.224, G.318, R.342 Ligands: A1L.23 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.195, B:D.219, B:P.223, B:W.224 pi-Stacking: B:W.224, B:W.224, B:W.224

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hirose, T. et al., Observation of the controlled assembly of preclick components in the in situ click chemistry generation of a chitinase inhibitor. Proc.Natl.Acad.Sci.USA (2013)

Release Date

2013-09-18

Peptides

Chitinase B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Chitinase B

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