SMTL ID : 8yui.1 (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: 14 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.11, GOL.23, GOL.30 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:P.220, A:W.221 Hydrogen bonds: A:R.295, A:R.295, A:D.317, A:D.317 Water bridges: A:R.339, A:R.339

34 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: R.163, A.205, P.206, L.207, D.208, K.285 Ligand excluded by PLIP GOL.3: 6 residues within 4Å: Chain A: T.4, R.5, T.46, H.47, R.90 Ligands: GOL.16 Ligand excluded by PLIP GOL.4: 6 residues within 4Å: Chain A: P.261, F.264, S.265, R.440, Y.441, T.442 Ligand excluded by PLIP GOL.5: 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.6: 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.7: 7 residues within 4Å: Chain A: K.394, Y.422, Y.428, D.429, D.430, S.431 Ligands: ACT.33 Ligand excluded by PLIP GOL.8: 4 residues within 4Å: Chain A: W.360, N.361, D.362, K.363 Ligand excluded by PLIP GOL.9: 4 residues within 4Å: Chain A: A.456, S.470, Y.471, Q.472 Ligand excluded by PLIP GOL.10: 3 residues within 4Å: Chain A: G.352, N.353, Y.354 Ligand excluded by PLIP GOL.12: 4 residues within 4Å: Chain A: F.191, F.192, R.195 Ligands: GOL.35 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: 4 residues within 4Å: Chain A: R.121, D.153, A.157 Ligands: GOL.38 Ligand excluded by PLIP GOL.15: 6 residues within 4Å: Chain A: F.232, Y.392, Q.395, Q.396, M.435, R.440 Ligand excluded by PLIP GOL.16: 5 residues within 4Å: Chain A: R.90, A.177, P.179, Q.181 Ligands: GOL.3 Ligand excluded by PLIP GOL.17: 4 residues within 4Å: Chain A: T.164, Q.168, I.171 Ligands: GOL.18 Ligand excluded by PLIP GOL.18: 5 residues within 4Å: Chain A: Q.160, R.163, T.164, N.167 Ligands: GOL.17 Ligand excluded by PLIP GOL.19: 5 residues within 4Å: Chain A: R.245, T.257, F.260, P.261, S.262 Ligand excluded by PLIP GOL.20: 6 residues within 4Å: Chain A: G.328, D.330, E.331, Q.345, Q.348 Ligands: PO4.48 Ligand excluded by PLIP GOL.21: 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.22: 4 residues within 4Å: Chain A: Y.343, R.358, Y.380, D.382 Ligand excluded by PLIP GOL.23: 5 residues within 4Å: Chain A: W.221 Ligands: NAG-NAG.1, GOL.24, ACT.31, GOL.39 Ligand excluded by PLIP GOL.24: 9 residues within 4Å: Chain A: D.216, L.217, A.218, W.221, E.222, F.240, L.266 Ligands: GOL.23, GOL.39 Ligand excluded by PLIP GOL.25: 5 residues within 4Å: Chain A: R.358, W.360, E.384, Y.388 Ligands: ACT.42 Ligand excluded by PLIP GOL.26: 4 residues within 4Å: Chain A: G.250, W.251, S.252, E.255 Ligand excluded by PLIP GOL.27: 4 residues within 4Å: Chain A: S.198, L.249, W.251, M.278 Ligand excluded by PLIP GOL.29: 2 residues within 4Å: Chain A: P.282, S.283 Ligand excluded by PLIP GOL.30: 8 residues within 4Å: Chain A: D.216, Y.293, R.295, I.340, W.404, Q.408 Ligands: NAG-NAG.1, NGO.11 Ligand excluded by PLIP GOL.35: 5 residues within 4Å: Chain A: Q.148, A.149, S.194, R.195 Ligands: GOL.12 Ligand excluded by PLIP GOL.37: 4 residues within 4Å: Chain A: D.420, R.421, N.424, A.425 Ligand excluded by PLIP GOL.38: 6 residues within 4Å: Chain A: K.116, R.121, A.150, D.153, G.154 Ligands: GOL.14 Ligand excluded by PLIP GOL.39: 4 residues within 4Å: Chain A: F.191, E.222 Ligands: GOL.23, GOL.24 Ligand excluded by PLIP GOL.43: 5 residues within 4Å: Chain A: N.17, Q.18, S.28, V.29, R.334 Ligand excluded by PLIP GOL.45: 3 residues within 4Å: Chain A: S.57, V.106, N.110 Ligand excluded by PLIP GOL.46: 3 residues within 4Å: Chain A: W.480, G.481, Y.482 Ligand excluded by PLIP

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

NGO.11: 15 residues within 4Å: Chain A: Y.11, F.52, G.97, W.98, D.143, E.145, A.185, M.213, Y.215, D.216, Y.293, W.404 Ligands: NAG-NAG.1, NAG-NAG.1, GOL.30 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.11, A:A.185 Hydrogen bonds: A:W.98, A:E.145, A:D.216 Water bridges: A:Y.99

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

ACT.28: 2 residues within 4Å: Chain A: E.24, R.78 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.24 Water bridges: A:E.24, A:R.78 Salt bridges: A:R.78 ACT.31: 2 residues within 4Å: Chain A: W.221 Ligands: GOL.23 No protein-ligand interaction detected (PLIP) ACT.32: 3 residues within 4Å: Chain A: T.80, K.83, G.136 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.175 Salt bridges: A:K.83 ACT.33: 5 residues within 4Å: Chain A: F.423, N.424, A.425, A.426 Ligands: GOL.7 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.425 ACT.34: 4 residues within 4Å: Chain A: G.302, G.303, Y.370, A.372 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.303, A:Y.370 ACT.36: 3 residues within 4Å: Chain A: K.387, R.421, Y.428 6 PLIP interactions: 6 interactions with chain A Water bridges: A:K.387, A:K.387, A:Y.422, A:Y.422 Salt bridges: A:K.387, A:R.421 ACT.40: 4 residues within 4Å: Chain A: K.391, Q.395, S.431, L.433 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.395 Salt bridges: A:K.391 ACT.41: 5 residues within 4Å: Chain A: E.60, C.61, A.62, R.130, I.131 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.130 Water bridges: A:N.56 ACT.42: 4 residues within 4Å: Chain A: E.384, K.387, L.433 Ligands: GOL.25 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.384 Water bridges: A:K.387, A:K.387 Salt bridges: A:K.387 ACT.44: 4 residues within 4Å: Chain A: N.248, L.249, G.250 Ligands: ACT.49 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.248, A:N.248 ACT.49: 3 residues within 4Å: Chain A: K.199, N.248 Ligands: ACT.44 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.248 Water bridges: A:D.153, A:K.199 Salt bridges: A:K.199

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

PO4.47: 3 residues within 4Å: Chain A: K.43, A.84, H.85 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.43, A:H.85 PO4.48: 4 residues within 4Å: Chain A: D.330, E.331, R.334 Ligands: GOL.20 3 PLIP interactions: 3 interactions with chain A Water bridges: A:T.27, A:R.334, A:R.334

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
A

Chitinase B

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