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

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

monomer

Ligands

2 x NAA- NAA: 2-acetamido-2-deoxy-beta-D-allopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-allopyranose(Non-covalent)

NAA-NAA.1: 13 residues within 4Å: Chain A: F.13, P.15, F.52, G.97, W.98, Y.99, R.295, D.317, I.340, W.404 Ligands: NAA-NAA.2, AMI.26, ACT.45 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.99 NAA-NAA.2: 13 residues within 4Å: Chain A: W.98, E.145, Y.146, F.192, D.216, W.221, R.295, G.315, D.317 Ligands: NAA-NAA.1, NAA-NAA.1, AMI.28, ACT.42 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.317 Water bridges: A:R.295, A:R.295, A:R.295

27 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: K.394, Y.422, Y.428, D.429, D.430, S.431 Ligands: ACT.30, ACT.40 Ligand excluded by PLIP GOL.4: 7 residues within 4Å: Chain A: T.4, R.5, T.46, H.47, S.88, R.90 Ligands: GOL.12 Ligand excluded by PLIP GOL.5: 5 residues within 4Å: Chain A: Q.160, R.163, T.164, N.167 Ligands: GOL.11 Ligand excluded by PLIP GOL.6: 3 residues within 4Å: Chain A: P.314, G.315, E.316 Ligand excluded by PLIP GOL.7: 5 residues within 4Å: Chain A: R.245, T.257, F.260, P.261, S.262 Ligand excluded by PLIP GOL.8: 6 residues within 4Å: Chain A: P.261, F.264, S.265, R.440, Y.441, T.442 Ligand excluded by PLIP GOL.9: 6 residues within 4Å: Chain A: R.163, A.205, P.206, L.207, D.208, K.285 Ligand excluded by PLIP GOL.10: 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.11: 4 residues within 4Å: Chain A: T.164, N.167, Q.168 Ligands: GOL.5 Ligand excluded by PLIP GOL.12: 5 residues within 4Å: Chain A: R.90, A.177, P.179, Q.181 Ligands: GOL.4 Ligand excluded by PLIP GOL.13: 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.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: 3 residues within 4Å: Chain A: L.350, Q.357, R.358 Ligand excluded by PLIP GOL.17: 2 residues within 4Å: Chain A: R.411, N.412 Ligand excluded by PLIP GOL.18: 4 residues within 4Å: Chain A: Q.148, A.149, S.194, R.195 Ligand excluded by PLIP GOL.19: 4 residues within 4Å: Chain A: D.153, K.199, N.248 Ligands: ACT.48 Ligand excluded by PLIP GOL.20: 6 residues within 4Å: Chain A: S.198, L.249, W.251, M.278 Ligands: PO4.14, ACT.41 Ligand excluded by PLIP GOL.21: 5 residues within 4Å: Chain A: R.358, W.360, E.384, Y.388 Ligands: ACT.24 Ligand excluded by PLIP GOL.22: 5 residues within 4Å: Chain A: Y.343, E.347, R.358, Y.380, D.382 Ligand excluded by PLIP GOL.31: 3 residues within 4Å: Chain A: N.36, K.41, R.411 Ligand excluded by PLIP GOL.33: 5 residues within 4Å: Chain A: R.5, K.43, D.420, N.424 Ligands: ACT.47 Ligand excluded by PLIP GOL.35: 5 residues within 4Å: Chain A: K.391, Q.395, S.431 Ligands: ACT.34, ACT.40 Ligand excluded by PLIP GOL.43: 7 residues within 4Å: Chain A: M.278, E.279, G.280, V.281, P.282, G.447 Ligands: ACT.46 Ligand excluded by PLIP GOL.44: 7 residues within 4Å: Chain A: D.54, D.64, P.65, Y.100, V.106, S.107 Ligands: ACT.45 Ligand excluded by PLIP GOL.51: 1 residues within 4Å: Chain A: D.323 Ligand excluded by PLIP GOL.52: 5 residues within 4Å: Chain A: G.250, W.251, S.252, E.255 Ligands: ACT.41 Ligand excluded by PLIP GOL.53: 4 residues within 4Å: Chain A: W.360, N.361, D.362, K.363 Ligand excluded by PLIP

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

PO4.14: 4 residues within 4Å: Chain A: N.248, L.249, G.250 Ligands: GOL.20 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.248 PO4.32: 3 residues within 4Å: Chain A: K.387, R.421, Y.428 7 PLIP interactions: 7 interactions with chain A Water bridges: A:E.384, A:K.387, A:K.387, A:K.387, A:Y.422 Salt bridges: A:K.387, A:R.421

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

ACT.23: 2 residues within 4Å: Chain A: R.258, T.442 Ligand excluded by PLIP ACT.24: 3 residues within 4Å: Chain A: E.384, Y.388 Ligands: GOL.21 Ligand excluded by PLIP ACT.25: 1 residues within 4Å: Chain A: R.78 Ligand excluded by PLIP ACT.27: 8 residues within 4Å: Chain A: D.216, L.217, A.218, W.221, E.222, F.240, L.266 Ligands: AMI.28 Ligand excluded by PLIP ACT.29: 2 residues within 4Å: Chain A: K.43, H.85 Ligand excluded by PLIP ACT.30: 5 residues within 4Å: Chain A: F.423, N.424, A.425, A.426 Ligands: GOL.3 Ligand excluded by PLIP ACT.34: 4 residues within 4Å: Chain A: S.431, Q.432, L.433 Ligands: GOL.35 Ligand excluded by PLIP ACT.36: 3 residues within 4Å: Chain A: G.303, Y.370, A.372 Ligand excluded by PLIP ACT.37: 5 residues within 4Å: Chain A: G.328, D.330, E.331, Q.345, Q.348 Ligand excluded by PLIP ACT.38: 6 residues within 4Å: Chain A: P.318, Y.319, N.321, A.322, Y.324, K.336 Ligand excluded by PLIP ACT.39: 5 residues within 4Å: Chain A: G.105, V.106, S.107, H.108, A.109 Ligand excluded by PLIP ACT.40: 6 residues within 4Å: Chain A: K.391, K.394, D.430, S.431 Ligands: GOL.3, GOL.35 Ligand excluded by PLIP ACT.41: 5 residues within 4Å: Chain A: W.251, E.279, P.446 Ligands: GOL.20, GOL.52 Ligand excluded by PLIP ACT.42: 4 residues within 4Å: Chain A: F.191, F.192 Ligands: NAA-NAA.2, AMI.28 Ligand excluded by PLIP ACT.45: 5 residues within 4Å: Chain A: T.16, D.64, Y.100 Ligands: NAA-NAA.1, GOL.44 Ligand excluded by PLIP ACT.46: 3 residues within 4Å: Chain A: P.282, S.283 Ligands: GOL.43 Ligand excluded by PLIP ACT.47: 4 residues within 4Å: Chain A: D.420, N.424, A.425 Ligands: GOL.33 Ligand excluded by PLIP ACT.48: 4 residues within 4Å: Chain A: A.149, S.198, N.248 Ligands: GOL.19 Ligand excluded by PLIP ACT.49: 2 residues within 4Å: Chain A: Y.241, P.263 Ligand excluded by PLIP ACT.50: 1 residues within 4Å: Chain A: G.460 Ligand excluded by PLIP ACT.54: 1 residues within 4Å: Chain A: R.73 Ligand excluded by PLIP

2 x AMI: ALLOSAMIZOLINE(Non-covalent)

AMI.26: 14 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, M.402, W.404 Ligands: NAA-NAA.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.404 Hydrogen bonds: A:W.98, A:D.216 Water bridges: A:R.295 AMI.28: 15 residues within 4Å: Chain A: Y.146, A.187, G.188, G.189, A.190, F.191, F.192, M.213, Y.215, D.216, L.217, W.221 Ligands: NAA-NAA.2, ACT.27, ACT.42 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.192 Hydrogen bonds: A:G.188, A:G.189, A:M.213 Water bridges: A:W.221

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 allosamidin. To Be Published

Release Date

2025-04-02

Peptides

Chitinase B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Chitinase B

Related Entries With Identical Sequence