SMTL ID : 8yui.2 (1 other biounit)

X-ray Crystal structure of glycoside hydrolase family 18 chitinase from Serratia marcescens hexahistigine-tagged SmChiB with triacetyl chitotriose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.43 Å

Oligo State

monomer

Ligands

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

NAG-NAG.1: 13 residues within 4Å: Chain A: W.98, E.145, Y.146, F.192, M.213, D.216, P.220, W.221, R.295, G.315, D.317 Ligands: NGO.12, GOL.24 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.220 Hydrogen bonds: A:R.295, A:R.295, A:D.317, A:D.317 Water bridges: A:R.339, A:R.339

32 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: R.245, T.257, F.260, P.261, S.262 Ligands: GOL.3 Ligand excluded by PLIP GOL.3: 4 residues within 4Å: Chain A: R.245, S.262, P.263 Ligands: GOL.2 Ligand excluded by PLIP GOL.4: 5 residues within 4Å: Chain A: P.220, T.313, P.314, G.315, E.316 Ligand excluded by PLIP GOL.5: 7 residues within 4Å: Chain A: T.4, R.5, T.46, H.47, R.90, Y.209 Ligands: GOL.19 Ligand excluded by PLIP GOL.6: 6 residues within 4Å: Chain A: P.261, F.264, S.265, R.440, Y.441, T.442 Ligand excluded by PLIP GOL.7: 7 residues within 4Å: Chain A: Y.324, L.326, V.327, G.328, C.329, D.330, V.333 Ligand excluded by PLIP GOL.8: 7 residues within 4Å: Chain A: K.394, Y.422, Y.428, D.429, D.430, S.431 Ligands: ACT.31 Ligand excluded by PLIP GOL.10: 3 residues within 4Å: Chain A: L.350, Q.357, R.358 Ligand excluded by PLIP GOL.11: 2 residues within 4Å: Chain A: R.411, N.412 Ligand excluded by PLIP GOL.13: 4 residues within 4Å: Chain A: N.36, T.38, K.41, R.411 Ligand excluded by PLIP GOL.14: 5 residues within 4Å: Chain A: Q.148, A.149, S.194, R.195 Ligands: GOL.26 Ligand excluded by PLIP GOL.15: 4 residues within 4Å: Chain A: G.250, W.251, S.252, E.255 Ligand excluded by PLIP GOL.16: 4 residues within 4Å: Chain A: W.360, N.361, D.362, K.363 Ligand excluded by PLIP GOL.17: 4 residues within 4Å: Chain A: Y.343, R.358, Y.380, D.382 Ligand excluded by PLIP GOL.18: 6 residues within 4Å: Chain A: F.232, Y.392, Q.395, Q.396, M.435, R.440 Ligand excluded by PLIP GOL.19: 5 residues within 4Å: Chain A: R.90, A.177, P.179, Q.181 Ligands: GOL.5 Ligand excluded by PLIP GOL.20: 7 residues within 4Å: Chain A: F.13, I.14, P.15, T.16, S.51, F.52, Y.100 Ligand excluded by PLIP GOL.21: 6 residues within 4Å: Chain A: R.163, A.205, P.206, L.207, D.208, K.285 Ligand excluded by PLIP GOL.22: 4 residues within 4Å: Chain A: Q.160, R.163, T.164, N.167 Ligand excluded by PLIP GOL.23: 8 residues within 4Å: Chain A: F.191, D.216, L.217, A.218, W.221, E.222, L.266 Ligands: GOL.24 Ligand excluded by PLIP GOL.24: 5 residues within 4Å: Chain A: F.192, W.221 Ligands: NAG-NAG.1, GOL.23, ACT.36 Ligand excluded by PLIP GOL.25: 5 residues within 4Å: Chain A: R.358, W.360, E.384, Y.388 Ligands: ACT.40 Ligand excluded by PLIP GOL.26: 4 residues within 4Å: Chain A: F.191, F.192, R.195 Ligands: GOL.14 Ligand excluded by PLIP GOL.27: 8 residues within 4Å: Chain A: E.255, R.258, V.444, G.445, L.449, L.494, K.495, V.496 Ligand excluded by PLIP GOL.28: 3 residues within 4Å: Chain A: S.198, L.249, W.251 Ligand excluded by PLIP GOL.30: 4 residues within 4Å: Chain A: P.39, K.43, A.84, H.85 Ligand excluded by PLIP GOL.34: 6 residues within 4Å: Chain A: K.116, R.121, A.150, D.153, G.154 Ligands: GOL.35 Ligand excluded by PLIP GOL.35: 4 residues within 4Å: Chain A: R.121, D.153, A.157 Ligands: GOL.34 Ligand excluded by PLIP GOL.38: 4 residues within 4Å: Chain A: D.420, R.421, N.424, A.425 Ligand excluded by PLIP GOL.41: 5 residues within 4Å: Chain A: N.17, Q.18, S.28, V.29, R.334 Ligand excluded by PLIP GOL.43: 2 residues within 4Å: Chain A: S.57, N.110 Ligand excluded by PLIP GOL.47: 3 residues within 4Å: Chain A: V.281, P.282, S.283 Ligand excluded by PLIP

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.9: 4 residues within 4Å: Chain A: N.248, L.249, G.250 Ligands: ACT.42 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.248, A:N.248 PO4.45: 2 residues within 4Å: Chain A: D.330, E.331 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.334, A:R.334

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

NGO.12: 14 residues within 4Å: Chain A: Y.11, F.52, G.97, W.98, E.145, A.185, M.213, Y.215, D.216, Y.293, R.295, W.404 Ligands: NAG-NAG.1, NAG-NAG.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.11, A:A.185 Hydrogen bonds: A:W.98, A:Y.215, A:D.216, A:R.295 Water bridges: A:Y.99

11 x ACT: ACETATE ION(Non-functional Binders)

ACT.29: 2 residues within 4Å: Chain A: E.24, R.78 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.24, A:E.24 Salt bridges: A:R.78 ACT.31: 5 residues within 4Å: Chain A: F.423, N.424, A.425, A.426 Ligands: GOL.8 2 PLIP interactions: 2 interactions with chain A Water bridges: A:F.423, A:A.425 ACT.32: 3 residues within 4Å: Chain A: K.387, R.421, Y.428 5 PLIP interactions: 5 interactions with chain A Water bridges: A:K.387, A:K.387, A:Y.422 Salt bridges: A:K.387, A:R.421 ACT.33: 3 residues within 4Å: Chain A: T.80, K.83, G.136 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.80, A:T.80 Water bridges: A:K.83, A:R.175 Salt bridges: A:K.83 ACT.36: 2 residues within 4Å: Chain A: W.221 Ligands: GOL.24 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.221 ACT.37: 3 residues within 4Å: Chain A: G.436, T.437, R.440 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.436 Salt bridges: A:R.440 ACT.39: 4 residues within 4Å: Chain A: E.60, C.61, A.62, R.130 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.56 Salt bridges: A:R.130 ACT.40: 4 residues within 4Å: Chain A: E.384, K.387, Y.388 Ligands: GOL.25 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.387 Salt bridges: A:K.387 ACT.42: 3 residues within 4Å: Chain A: K.199, N.248 Ligands: PO4.9 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.248 Water bridges: A:D.153, A:S.198, A:K.199 Salt bridges: A:K.199 ACT.44: 3 residues within 4Å: Chain A: G.302, G.303, Y.370 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.303 ACT.46: 4 residues within 4Å: Chain A: K.391, Q.395, S.431, L.433 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.395, A:S.431 Salt bridges: A:K.391

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ebi, S. et al., X-ray Crystal structure of glycoside hydrolase family 18 chitinase from Serratia marcescens hexahistigine-tagged SmChiB with triacetyl chitotriose. To Be Published

Release Date

2025-04-02

Peptides

Chitinase B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Chitinase B

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