SMTL ID : 4b16.1

crystal structure of tamarind chitinase like lectin (TCLL) complexed with N-acetyl glucosamine (GlcNAc)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.61 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-functional Binders)

NAG-NAG.1: 5 residues within 4Å: Chain A: L.139, N.140, R.146, R.147, I.148 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain B: L.139, N.140, R.146, R.147, I.148 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 2 residues within 4Å: Chain A: G.1, R.266 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.1, A:G.1 GOL.9: 2 residues within 4Å: Chain B: G.1, R.266 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.1, B:G.1

2 x ACT: ACETATE ION(Non-covalent)(Non-functional Binders)

ACT.3: 7 residues within 4Å: Chain A: T.218, Y.253, F.254, F.257, R.258 Chain B: P.83 Ligands: NA.7 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.253, A:F.254, A:F.257, B:P.83 Hydrogen bonds: A:T.218 Water bridges: A:Y.253, A:Y.253, A:R.258 Salt bridges: A:R.258 ACT.10: 7 residues within 4Å: Chain A: P.83 Chain B: T.218, Y.253, F.254, F.257, R.258 Ligands: NA.14 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.253, B:F.254, B:F.257, A:P.83 Water bridges: B:Y.253, B:R.258 Salt bridges: B:R.258

4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Post Translational Modification)

NAG.4: 7 residues within 4Å: Chain A: K.65, Q.68, L.69, E.113, V.114, Y.115, R.146 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.69 Hydrogen bonds: A:K.65, A:E.113, A:Y.115, A:R.146, A:R.146 Salt bridges: A:K.65 NAG.5: 5 residues within 4Å: Chain A: P.125, E.126, G.127, Y.161, Y.162 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.126, A:Y.162 Water bridges: A:G.127, A:Y.161 NAG.11: 7 residues within 4Å: Chain B: K.65, Q.68, L.69, E.113, V.114, Y.115, R.146 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.69 Hydrogen bonds: B:K.65, B:E.113, B:Y.115, B:R.146, B:R.146 Salt bridges: B:K.65 NAG.12: 5 residues within 4Å: Chain B: P.125, E.126, G.127, Y.161, Y.162 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.126, B:Y.162 Water bridges: B:G.127, B:Y.161, B:Y.161, B:Y.161

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)(Post Translational Modification)

MPD.6: 6 residues within 4Å: Chain A: F.196, M.199, K.200, A.237, Q.240, A.241 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.196, A:M.199, A:K.200 Hydrogen bonds: A:A.241 Water bridges: A:T.203 MPD.13: 6 residues within 4Å: Chain B: F.196, M.199, K.200, A.237, Q.240, A.241 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.196, B:M.199, B:K.200 Hydrogen bonds: B:A.241 Water bridges: B:T.203, B:T.203

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

NA.7: 6 residues within 4Å: Chain A: T.218, D.220, F.254, R.258 Chain B: P.125 Ligands: ACT.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.218, A:D.220, A:R.258 NA.14: 6 residues within 4Å: Chain A: P.125 Chain B: T.218, D.220, F.254, R.258 Ligands: ACT.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.218, B:R.258

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Patil, D.N. et al., Structural Investigation of a Novel N-Acetyl Glucosamine Binding Chi-Lectin which Reveals Evolutionary Relationship with Class III Chitinases. Plos One (2013)

Release Date

2013-06-12

Peptides

CHITINASE LIKE LECTIN: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

CHITINASE LIKE LECTIN

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