SMTL ID : 4tx8.2 (1 other biounit)

Crystal Structure of a Family GH18 Chitinase from Chromobacterium violaceum

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

homo-dimer

Ligands

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.1: 5 residues within 4Å: Chain A: C.26, N.47, G.75, S.76, C.77 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.47, A:C.77 NAG.8: 5 residues within 4Å: Chain B: C.26, N.47, G.75, S.76, C.77 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.47, B:C.77

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: R.353, A.356, F.360 Ligands: MG.9 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:R.353, A:A.356, H2O.2, H2O.3, H2O.3, H2O.13 MG.9: 4 residues within 4Å: Chain B: R.353, A.356, F.360 Ligands: MG.2 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:R.353, B:A.356, H2O.2, H2O.13, H2O.14, H2O.14

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: D.218, E.220, A.255, P.256, Q.292 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.218, A:E.220, A:E.220, A:A.255, H2O.5 CA.10: 5 residues within 4Å: Chain B: D.218, E.220, A.255, P.256, Q.292 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.218, B:E.220, B:E.220, B:A.255, H2O.17

8 x FLC: CITRATE ANION(Non-covalent)

FLC.4: 11 residues within 4Å: Chain A: E.257, N.295, N.296, N.357, S.358 Chain B: A.65, A.66, S.67, P.68, P.119, W.401 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:N.295, A:N.357, B:P.119 Hydrogen bonds: A:S.358, B:A.66, B:A.66 Water bridges: A:N.295, A:N.296 FLC.5: 6 residues within 4Å: Chain A: F.140, Q.292, Y.294, N.295, W.397 Ligands: FLC.6 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.397 Hydrogen bonds: A:Q.292, A:N.295, A:S.355 Water bridges: A:Q.292, A:Q.292, A:Q.292, A:Q.292, A:Q.292 FLC.6: 11 residues within 4Å: Chain A: F.140, G.182, G.183, D.218, S.221, G.222, E.257 Chain B: A.117, N.118, P.119 Ligands: FLC.5 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.183, A:D.218, A:S.221, A:S.221, A:S.221, A:S.221, A:G.222 Water bridges: B:A.117, B:A.117 FLC.7: 6 residues within 4Å: Chain A: G.311, S.312, A.313, D.314, T.365, K.368 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.313 Hydrogen bonds: A:G.311, A:A.313, A:D.314, A:K.368 Water bridges: A:G.380 Salt bridges: A:K.368, A:K.368 FLC.11: 11 residues within 4Å: Chain A: A.65, A.66, S.67, P.68, P.119, W.401 Chain B: E.257, N.295, N.296, N.357, S.358 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:P.119, B:N.295, B:N.357 Hydrogen bonds: A:A.66, A:A.66, B:S.358 Water bridges: B:N.295, B:N.296 FLC.12: 6 residues within 4Å: Chain B: F.140, Q.292, Y.294, N.295, W.397 Ligands: FLC.13 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:W.397 Hydrogen bonds: B:Q.292, B:Y.294, B:N.295, B:S.355 Water bridges: B:E.257, B:Q.292, B:Q.292, B:Q.292, B:Q.292 FLC.13: 11 residues within 4Å: Chain A: A.117, N.118, P.119 Chain B: F.140, G.182, G.183, D.218, S.221, G.222, E.257 Ligands: FLC.12 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.183, B:D.218, B:S.221, B:S.221, B:S.221, B:S.221, B:G.222 Water bridges: B:E.257, B:E.257, A:A.117, A:A.117 FLC.14: 6 residues within 4Å: Chain B: G.311, S.312, A.313, D.314, T.365, K.368 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:A.313 Hydrogen bonds: B:G.311, B:A.313, B:D.314, B:K.368 Water bridges: B:T.365, B:G.380 Salt bridges: B:K.368, B:K.368

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pereira, H.M. et al., Crystal Structure of a Family GH18 Chitinase from Chromobacterium violaceum. To Be Published

Release Date

2015-10-14

Peptides

Probable chitinase A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Probable chitinase A

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