SMTL ID : 8yug.1

X-ray Crystal structure of glycoside hydrolase family 18 chitinase from Serratia marcescens hexahistigine-tagged SmChiB apo enzyme

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.71 Å

Oligo State

monomer

Ligands

35 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 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.2: 9 residues within 4Å: Chain A: F.191, D.216, L.217, A.218, W.221, E.222, L.266 Ligands: GOL.16, GOL.50 Ligand excluded by PLIP GOL.3: 6 residues within 4Å: Chain A: R.163, A.205, P.206, L.207, D.208, K.285 Ligand excluded by PLIP GOL.5: 6 residues within 4Å: Chain A: P.261, F.264, S.265, R.440, Y.441, T.442 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: 6 residues within 4Å: Chain A: R.245, T.257, F.260, P.261, S.262 Ligands: ACT.46 Ligand excluded by PLIP GOL.10: 1 residues within 4Å: Chain A: N.412 Ligand excluded by PLIP GOL.11: 4 residues within 4Å: Chain A: Q.160, R.163, T.164, N.167 Ligand excluded by PLIP GOL.12: 7 residues within 4Å: Chain A: K.394, Y.422, Y.428, D.429, D.430, S.431 Ligands: ACT.42 Ligand excluded by PLIP GOL.14: 4 residues within 4Å: Chain A: W.360, N.361, D.362, K.363 Ligand excluded by PLIP GOL.15: 4 residues within 4Å: Chain A: A.464, Q.465, G.481, Y.482 Ligand excluded by PLIP GOL.16: 6 residues within 4Å: Chain A: F.192, W.221 Ligands: GOL.2, GOL.28, GOL.47, GOL.50 Ligand excluded by PLIP GOL.18: 5 residues within 4Å: Chain A: K.116, R.121, A.150, D.153, G.154 Ligand excluded by PLIP GOL.19: 6 residues within 4Å: Chain A: P.220, R.295, D.337, R.339, I.340 Ligands: GOL.28 Ligand excluded by PLIP GOL.20: 6 residues within 4Å: Chain A: F.232, Y.392, Q.395, Q.396, M.435, R.440 Ligand excluded by PLIP GOL.21: 6 residues within 4Å: Chain A: Y.343, E.347, L.350, R.358, Y.380, D.382 Ligand excluded by PLIP GOL.23: 3 residues within 4Å: Chain A: K.83, R.175 Ligands: ACT.45 Ligand excluded by PLIP GOL.24: 5 residues within 4Å: Chain A: P.15, N.17, Q.18, S.28, V.29 Ligand excluded by PLIP GOL.25: 3 residues within 4Å: Chain A: P.39, K.43, H.85 Ligand excluded by PLIP GOL.26: 6 residues within 4Å: Chain A: D.54, D.64, P.65, Y.99, Y.100, S.107 Ligand excluded by PLIP GOL.27: 7 residues within 4Å: Chain A: Y.215, D.216, Y.293, R.295, W.404 Ligands: ACT.4, GOL.28 Ligand excluded by PLIP GOL.28: 5 residues within 4Å: Chain A: W.98, D.216 Ligands: GOL.16, GOL.19, GOL.27 Ligand excluded by PLIP GOL.29: 6 residues within 4Å: Chain A: N.77, K.133, D.134, Y.135, G.136 Ligands: ACT.45 Ligand excluded by PLIP GOL.30: 5 residues within 4Å: Chain A: Q.148, A.149, S.194, R.195 Ligands: GOL.31 Ligand excluded by PLIP GOL.31: 4 residues within 4Å: Chain A: F.191, F.192, R.195 Ligands: GOL.30 Ligand excluded by PLIP GOL.32: 3 residues within 4Å: Chain A: E.246, A.247, N.248 Ligand excluded by PLIP GOL.33: 7 residues within 4Å: Chain A: T.4, R.5, T.46, H.47, R.90, Y.209 Ligands: ACT.8 Ligand excluded by PLIP GOL.47: 4 residues within 4Å: Chain A: W.221, E.222 Ligands: GOL.16, GOL.50 Ligand excluded by PLIP GOL.48: 5 residues within 4Å: Chain A: R.358, W.360, E.384, Y.388 Ligands: ACT.35 Ligand excluded by PLIP GOL.49: 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.50: 5 residues within 4Å: Chain A: F.191, E.222 Ligands: GOL.2, GOL.16, GOL.47 Ligand excluded by PLIP GOL.51: 3 residues within 4Å: Chain A: T.164, Q.168, I.171 Ligand excluded by PLIP GOL.52: 2 residues within 4Å: Chain A: D.323, W.325 Ligand excluded by PLIP GOL.53: 4 residues within 4Å: Chain A: S.198, L.249, W.251, P.446 Ligand excluded by PLIP GOL.54: 4 residues within 4Å: Chain A: R.5, K.43, D.420, N.424 Ligand excluded by PLIP

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

ACT.4: 7 residues within 4Å: Chain A: Y.11, D.143, E.145, A.185, M.213, Y.215 Ligands: GOL.27 Ligand excluded by PLIP ACT.8: 5 residues within 4Å: Chain A: R.90, A.177, P.179, Q.181 Ligands: GOL.33 Ligand excluded by PLIP ACT.34: 2 residues within 4Å: Chain A: D.330, E.331 Ligand excluded by PLIP ACT.35: 5 residues within 4Å: Chain A: E.384, K.387, Y.388, L.433 Ligands: GOL.48 Ligand excluded by PLIP ACT.36: 3 residues within 4Å: Chain A: G.305, Q.357 Ligands: ACT.43 Ligand excluded by PLIP ACT.37: 4 residues within 4Å: Chain A: T.27, N.36, R.344, R.411 Ligand excluded by PLIP ACT.38: 1 residues within 4Å: Chain A: R.78 Ligand excluded by PLIP ACT.39: 6 residues within 4Å: Chain A: E.60, C.61, A.62, S.127, R.130, I.131 Ligand excluded by PLIP ACT.40: 3 residues within 4Å: Chain A: T.117, A.119, A.120 Ligand excluded by PLIP ACT.41: 4 residues within 4Å: Chain A: N.248, L.249, G.250 Ligands: PO4.9 Ligand excluded by PLIP ACT.42: 4 residues within 4Å: Chain A: F.423, N.424, A.426 Ligands: GOL.12 Ligand excluded by PLIP ACT.43: 5 residues within 4Å: Chain A: G.302, G.303, Y.370, A.372 Ligands: ACT.36 Ligand excluded by PLIP ACT.44: 3 residues within 4Å: Chain A: R.258, T.442 Ligands: ACT.46 Ligand excluded by PLIP ACT.45: 5 residues within 4Å: Chain A: T.80, K.83, G.136 Ligands: GOL.23, GOL.29 Ligand excluded by PLIP ACT.46: 4 residues within 4Å: Chain A: T.257, P.261 Ligands: GOL.7, ACT.44 Ligand excluded by PLIP ACT.55: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

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

PO4.9: 3 residues within 4Å: Chain A: K.199, N.248 Ligands: ACT.41 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 PO4.13: 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:K.387, A:Y.422 Salt bridges: A:K.387, A:R.421 PO4.17: 2 residues within 4Å: Chain A: P.282, S.283 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.283 Water bridges: A:V.281, A:S.283, A:S.283, A:A.284 PO4.22: 5 residues within 4Å: Chain A: K.391, Q.395, S.431, L.433, M.435 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.395 Water bridges: A:Q.395, A:L.433 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 apo enzyme. 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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