SMTL ID : 5z7m.1

SmChiA sliding-intermediate with chitohexaose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x NDG- NAG- NAG- NAG- NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose

NDG-NAG-NAG-NAG-NAG-NAG.1: 20 residues within 4Å: Chain A: W.144, Y.147, R.149, F.168, I.184, S.187, H.206, D.207, F.209, W.252, T.253, F.293, Y.367, D.368, A.373, W.449, E.450 Ligands: GOL.2, NAG.17, NAG.18 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.207, A:D.368, A:D.368, A:D.368, A:D.368 Hydrophobic interactions: A:D.368 Water bridges: A:R.423, A:R.423, A:R.423

15 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 13 residues within 4Å: Chain A: D.368, F.369, Y.370, G.371, A.372, A.373, D.374, R.423 Ligands: NDG-NAG-NAG-NAG-NAG-NAG.1, NDG-NAG-NAG-NAG-NAG-NAG.1, GOL.3, NAG.17, NAG.18 Ligand excluded by PLIP GOL.3: 5 residues within 4Å: Chain A: F.369, Y.370, G.371, D.374 Ligands: GOL.2 Ligand excluded by PLIP GOL.4: 6 residues within 4Å: Chain A: E.124, R.149, N.150, F.151, K.155, R.457 Ligand excluded by PLIP GOL.5: 6 residues within 4Å: Chain A: F.15, A.16, E.19, K.34, A.37, D.38 Ligand excluded by PLIP GOL.6: 5 residues within 4Å: Chain A: N.59, K.81, G.82, R.84, Y.85 Ligand excluded by PLIP GOL.7: 3 residues within 4Å: Chain A: I.8, W.10, T.103 Ligand excluded by PLIP GOL.8: 5 residues within 4Å: Chain A: E.19, V.20, Q.22, D.223, P.225 Ligand excluded by PLIP GOL.9: 3 residues within 4Å: Chain A: C.195, R.198, D.200 Ligand excluded by PLIP GOL.10: 6 residues within 4Å: Chain A: Y.27, N.28, V.31, R.198, E.276, T.280 Ligand excluded by PLIP GOL.11: 5 residues within 4Å: Chain A: T.52, T.53, K.55, N.93, A.94 Ligand excluded by PLIP GOL.12: 1 residues within 4Å: Chain A: D.324 Ligand excluded by PLIP GOL.13: 6 residues within 4Å: Chain A: R.320, N.357, S.358, M.359, D.360, K.413 Ligand excluded by PLIP GOL.14: 2 residues within 4Å: Chain A: M.464, Y.470 Ligand excluded by PLIP GOL.15: 3 residues within 4Å: Chain A: N.429, G.430, Y.431 Ligand excluded by PLIP GOL.16: 6 residues within 4Å: Chain A: G.134, K.135, V.136, T.162, H.163, H.361 Ligand excluded by PLIP

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

NAG.17: 8 residues within 4Å: Chain A: W.252, F.293, D.368, A.373 Ligands: NDG-NAG-NAG-NAG-NAG-NAG.1, NDG-NAG-NAG-NAG-NAG-NAG.1, GOL.2, NAG.18 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.368, A:D.368, A:D.368, A:D.368 Water bridges: A:S.341, A:R.423, A:R.423, A:R.423 NAG.18: 7 residues within 4Å: Chain A: W.252, T.253 Ligands: NDG-NAG-NAG-NAG-NAG-NAG.1, NDG-NAG-NAG-NAG-NAG-NAG.1, NDG-NAG-NAG-NAG-NAG-NAG.1, GOL.2, NAG.17 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:W.252 Water bridges: A:W.252, A:W.252, A:W.252, A:R.423, A:R.423, A:R.423, A:R.423

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakamura, A. et al., Processive chitinase is Brownian monorail operated by fast catalysis after peeling rail from crystalline chitin. Nat Commun (2018)

Release Date

2018-09-26

Peptides

Chitinase A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Chitinase A

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