SMTL ID : 8yuh.1 (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: 12 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.27 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.13, A:P.15 NAA-NAA.2: 11 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, AMI.28 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.317 Water bridges: A:R.295, A:R.295, A:R.295

25 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.25, ACT.39 Ligand excluded by PLIP GOL.4: 7 residues within 4Å: Chain A: T.4, R.5, T.46, H.47, R.90, Y.209 Ligands: GOL.23 Ligand excluded by PLIP GOL.5: 3 residues within 4Å: Chain A: Q.160, R.163, T.164 Ligand excluded by PLIP GOL.6: 6 residues within 4Å: Chain A: R.163, A.205, P.206, L.207, D.208, K.285 Ligand excluded by PLIP GOL.7: 6 residues within 4Å: Chain A: P.261, F.264, S.265, R.440, Y.441, T.442 Ligand excluded by PLIP GOL.8: 5 residues within 4Å: Chain A: R.245, T.257, F.260, P.261, S.262 Ligand excluded by PLIP GOL.9: 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.10: 4 residues within 4Å: Chain A: F.191, F.192, R.195 Ligands: GOL.13 Ligand excluded by PLIP GOL.11: 10 residues within 4Å: Chain A: E.255, R.258, V.444, G.445, P.446, L.449, L.494, K.495, V.496 Ligands: ACT.48 Ligand excluded by PLIP GOL.12: 5 residues within 4Å: Chain A: N.77, K.133, D.134, Y.135, G.136 Ligand excluded by PLIP GOL.13: 5 residues within 4Å: Chain A: Q.148, A.149, S.194, R.195 Ligands: GOL.10 Ligand excluded by PLIP GOL.15: 4 residues within 4Å: Chain A: W.360, N.361, D.362, K.363 Ligand excluded by PLIP GOL.16: 6 residues within 4Å: Chain A: F.232, Y.392, Q.395, Q.396, M.435, R.440 Ligand excluded by PLIP GOL.18: 2 residues within 4Å: Chain A: E.222, F.240 Ligand excluded by PLIP GOL.19: 5 residues within 4Å: Chain A: S.198, L.249, W.251, M.278 Ligands: ACT.26 Ligand excluded by PLIP GOL.20: 4 residues within 4Å: Chain A: A.464, Q.465, G.481, Y.482 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.22: 5 residues within 4Å: Chain A: R.358, W.360, E.384, Y.388 Ligands: ACT.29 Ligand excluded by PLIP GOL.23: 5 residues within 4Å: Chain A: R.90, A.177, P.179, Q.181 Ligands: GOL.4 Ligand excluded by PLIP GOL.31: 3 residues within 4Å: Chain A: N.36, K.41, R.411 Ligand excluded by PLIP GOL.32: 5 residues within 4Å: Chain A: R.5, K.43, D.420, N.424 Ligands: ACT.46 Ligand excluded by PLIP GOL.42: 4 residues within 4Å: Chain A: I.224, Y.308, S.309, S.310 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.54: 5 residues within 4Å: Chain A: G.250, W.251, S.252, E.255 Ligands: ACT.48 Ligand excluded by PLIP GOL.57: 2 residues within 4Å: Chain A: D.323, W.325 Ligand excluded by PLIP

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

PO4.14: 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 PO4.17: 3 residues within 4Å: Chain A: K.387, R.421, Y.428 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.387 Salt bridges: A:K.387, A:R.421 PO4.55: 2 residues within 4Å: Chain A: E.24, R.78 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.24 Water bridges: A:E.24, A:D.74, A:R.78, A:R.78, A:R.78 Salt bridges: A:R.78 PO4.56: 4 residues within 4Å: Chain A: K.199, N.248 Ligands: ACT.26, ACT.59 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.248 Water bridges: A:D.153, A:K.199, A:N.248 Salt bridges: A:K.199

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

ACT.24: 2 residues within 4Å: Chain A: R.258, T.442 Ligand excluded by PLIP ACT.25: 5 residues within 4Å: Chain A: F.423, N.424, A.425, A.426 Ligands: GOL.3 Ligand excluded by PLIP ACT.26: 4 residues within 4Å: Chain A: N.248, L.249 Ligands: GOL.19, PO4.56 Ligand excluded by PLIP ACT.29: 4 residues within 4Å: Chain A: E.384, K.387, L.433 Ligands: GOL.22 Ligand excluded by PLIP ACT.30: 4 residues within 4Å: Chain A: D.330, E.331, R.334 Ligands: ACT.34 Ligand excluded by PLIP ACT.33: 4 residues within 4Å: Chain A: G.302, G.303, Y.370, A.372 Ligand excluded by PLIP ACT.34: 5 residues within 4Å: Chain A: D.330, E.331, Q.345, Q.348 Ligands: ACT.30 Ligand excluded by PLIP ACT.35: 6 residues within 4Å: Chain A: K.391, Q.395, S.431, L.433 Ligands: ACT.36, ACT.52 Ligand excluded by PLIP ACT.36: 4 residues within 4Å: Chain A: S.431, Q.432, D.434 Ligands: ACT.35 Ligand excluded by PLIP ACT.37: 1 residues within 4Å: Chain A: T.437 Ligand excluded by PLIP ACT.38: 5 residues within 4Å: Chain A: G.105, V.106, S.107, H.108, A.109 Ligand excluded by PLIP ACT.39: 7 residues within 4Å: Chain A: K.391, K.394, Q.395, D.430, S.431 Ligands: GOL.3, ACT.52 Ligand excluded by PLIP ACT.40: 5 residues within 4Å: Chain A: Y.319, N.321, A.322, Y.324, K.336 Ligand excluded by PLIP ACT.41: 3 residues within 4Å: Chain A: F.191, E.222 Ligands: ACT.53 Ligand excluded by PLIP ACT.43: 2 residues within 4Å: Chain A: P.282, S.283 Ligand excluded by PLIP ACT.45: 4 residues within 4Å: Chain A: T.16, D.64, Y.100 Ligands: GOL.44 Ligand excluded by PLIP ACT.46: 4 residues within 4Å: Chain A: D.420, N.424, A.425 Ligands: GOL.32 Ligand excluded by PLIP ACT.47: 2 residues within 4Å: Chain A: D.74, N.77 Ligand excluded by PLIP ACT.48: 5 residues within 4Å: Chain A: W.251, E.255, P.446 Ligands: GOL.11, GOL.54 Ligand excluded by PLIP ACT.49: 1 residues within 4Å: Chain A: A.322 Ligand excluded by PLIP ACT.50: 2 residues within 4Å: Chain A: E.279, G.280 Ligand excluded by PLIP ACT.51: 1 residues within 4Å: Chain A: N.353 Ligand excluded by PLIP ACT.52: 3 residues within 4Å: Chain A: Q.395 Ligands: ACT.35, ACT.39 Ligand excluded by PLIP ACT.53: 9 residues within 4Å: Chain A: D.216, L.217, A.218, W.221, E.222, F.240, L.266 Ligands: AMI.28, ACT.41 Ligand excluded by PLIP ACT.58: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP ACT.59: 4 residues within 4Å: Chain A: A.149, S.198, N.248 Ligands: PO4.56 Ligand excluded by PLIP ACT.60: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

2 x AMI: ALLOSAMIZOLINE(Non-covalent)

AMI.27: 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:Y.215, A:D.216 AMI.28: 14 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.53 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.192 Hydrogen bonds: A:G.188, A:G.189, A:M.213

Links

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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
A

Chitinase B

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