SMTL ID : 4hmd.1

Crystal structure of cold-adapted chitinase from Moritella marina with a reaction intermediate - oxazolinium ion (NGO)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.26 Å

Oligo State

homo-dimer

Ligands

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

NAG.1: 11 residues within 4Å: Chain A: W.18, R.22, Y.24, F.48, G.95, A.96, D.256, A.257, W.289, W.293 Ligands: NGO.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.24 Hydrogen bonds: A:A.96, A:A.96 Water bridges: A:R.22 NAG.5: 11 residues within 4Å: Chain B: W.18, R.22, Y.24, F.48, G.95, A.96, D.256, A.257, W.289, W.293 Ligands: NGO.6 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.24 Hydrogen bonds: B:A.96, B:A.96 Water bridges: B:R.22

2 x NGO: 2-METHYL-4,5-DIHYDRO-(1,2-DIDEOXY-ALPHA-D-GLUCOPYRANOSO)[2,1-D]-1,3-OXAZOLE(Non-covalent)

NGO.2: 13 residues within 4Å: Chain A: Y.14, Y.24, F.48, G.95, A.96, D.129, Q.196, Y.198, N.199, A.257, A.258, W.289 Ligands: NAG.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.14, A:W.289 Hydrogen bonds: A:Y.24, A:Y.24, A:A.96, A:Q.196, A:N.199 NGO.6: 13 residues within 4Å: Chain B: Y.14, Y.24, F.48, G.95, A.96, D.129, Q.196, Y.198, N.199, A.257, A.258, W.289 Ligands: NAG.5 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.14, B:W.289 Hydrogen bonds: B:Y.24, B:A.96, B:Q.196, B:Y.198, B:N.199

2 x NA: SODIUM ION(Non-functional Binders)

NA.3: 5 residues within 4Å: Chain A: T.2, N.83, G.122, F.123, D.124 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.83, A:F.123 NA.7: 5 residues within 4Å: Chain B: T.2, N.83, G.122, F.123, D.124 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.83, B:D.124 Water bridges: B:G.1

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: D.487, T.501, H.502, N.503, G.504 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.502, A:N.503, A:G.504 GOL.8: 5 residues within 4Å: Chain B: D.487, T.501, H.502, N.503, G.504 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.502, B:N.503, B:G.504

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malecki, P.H. et al., Structure of a complete four-domain chitinase from Moritella marina, a marine psychrophilic bacterium. Acta Crystallogr.,Sect.D (2013)

Release Date

2013-05-01

Peptides

Chitinase 60: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Chitinase 60

Related Entries With Identical Sequence