SMTL ID : 1dwi.1

Study on radiation damage on a cryocooled crystal. Part 5: Structure after irradiation with 54.0*10e15 photons/mm2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

4 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 6 residues within 4Å: Chain A: S.205, N.216, T.219, E.303, R.304, T.343 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:R.304 NAG-NAG.4: 7 residues within 4Å: Chain A: Y.262, N.263, D.264, N.359, A.360, S.361, H.363 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 6 residues within 4Å: Chain B: S.205, N.216, T.219, E.303, R.304, T.343 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:R.304 NAG-NAG.28: 7 residues within 4Å: Chain B: Y.262, N.263, D.264, N.359, A.360, S.361, H.363 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- XYP- FUC: beta-D-xylopyranose-(1-2)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-XYP-FUC.2: 5 residues within 4Å: Chain A: N.263, T.265, D.266, A.360, S.361 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-XYP-FUC.26: 5 residues within 4Å: Chain B: N.263, T.265, D.266, A.360, S.361 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- XYP- MAN- MAN- FUC: beta-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)][alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-XYP-MAN-MAN-FUC.3: 4 residues within 4Å: Chain A: N.290, T.292, Q.295, I.298 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.295, A:Q.295, A:Q.295 Water bridges: A:Q.295 NAG-NAG-BMA-XYP-MAN-MAN-FUC.27: 4 residues within 4Å: Chain B: N.290, T.292, Q.295, I.298 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.295, B:Q.295, B:Q.295 Water bridges: B:Q.295

12 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.5: 6 residues within 4Å: Chain A: T.15, D.16, A.17, N.19, S.22, P.499 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.499 Hydrogen bonds: A:D.16, A:N.19 Water bridges: A:A.17 NAG.6: 2 residues within 4Å: Chain A: N.88, S.498 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.88, A:S.498 NAG.7: 4 residues within 4Å: Chain A: K.163, D.237, L.238, N.242 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.238 Hydrogen bonds: A:N.242 Water bridges: A:N.242 NAG.8: 4 residues within 4Å: Chain A: Y.56, N.58, S.211 Ligands: SO4.18 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.211 NAG.9: 3 residues within 4Å: Chain A: S.342, N.344, M.349 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.342 NAG.10: 2 residues within 4Å: Chain A: N.480, D.483 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.480, A:D.483 Water bridges: A:T.482, A:D.483 NAG.29: 6 residues within 4Å: Chain B: T.15, D.16, A.17, N.19, S.22, P.499 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:P.499 Hydrogen bonds: B:N.19 Water bridges: B:A.17, B:P.499 NAG.30: 2 residues within 4Å: Chain B: N.88, S.498 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.88, B:S.498 NAG.31: 4 residues within 4Å: Chain B: K.163, D.237, L.238, N.242 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.238 Hydrogen bonds: B:N.242 Water bridges: B:N.242 NAG.32: 4 residues within 4Å: Chain B: Y.56, N.58, S.211 Ligands: SO4.42 1 PLIP interactions: 1 interactions with chain B Water bridges: B:S.211 NAG.33: 3 residues within 4Å: Chain B: S.342, N.344, M.349 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.342 NAG.34: 2 residues within 4Å: Chain B: N.480, D.483 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.480, B:D.483 Water bridges: B:T.482, B:D.483, B:D.483

2 x ZN: ZINC ION(Non-covalent)

ZN.11: 6 residues within 4Å: Chain A: H.54, D.68 Chain B: H.54, N.66, D.68 Ligands: ZN.35 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Metal complexes: B:H.54, B:D.68, B:D.68, A:H.54, A:D.68 ZN.35: 6 residues within 4Å: Chain A: H.54, N.66, D.68 Chain B: H.54, D.68 Ligands: ZN.11 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Metal complexes: B:H.54, B:D.68, A:H.54, A:D.68, A:D.68

16 x SO4: SULFATE ION(Non-functional Binders)

SO4.12: 4 residues within 4Å: Chain A: E.151, R.203 Chain B: R.104, R.109 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain A: K.106, R.109 Chain B: E.149 Ligand excluded by PLIP SO4.14: 4 residues within 4Å: Chain A: R.257, Q.331, L.355 Ligands: SO4.19 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain A: Q.5, E.6, N.7 Ligand excluded by PLIP SO4.16: 4 residues within 4Å: Chain A: R.267, H.268, A.271, R.275 Ligand excluded by PLIP SO4.17: 3 residues within 4Å: Chain A: R.107, V.111, E.171 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain A: N.58, H.64 Ligands: NAG.8 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain A: R.192, R.257 Ligands: SO4.14 Ligand excluded by PLIP SO4.36: 4 residues within 4Å: Chain A: R.104, R.109 Chain B: E.151, R.203 Ligand excluded by PLIP SO4.37: 3 residues within 4Å: Chain A: E.149 Chain B: K.106, R.109 Ligand excluded by PLIP SO4.38: 4 residues within 4Å: Chain B: R.257, Q.331, L.355 Ligands: SO4.43 Ligand excluded by PLIP SO4.39: 3 residues within 4Å: Chain B: Q.5, E.6, N.7 Ligand excluded by PLIP SO4.40: 4 residues within 4Å: Chain B: R.267, H.268, A.271, R.275 Ligand excluded by PLIP SO4.41: 3 residues within 4Å: Chain B: R.107, V.111, E.171 Ligand excluded by PLIP SO4.42: 3 residues within 4Å: Chain B: N.58, H.64 Ligands: NAG.32 Ligand excluded by PLIP SO4.43: 3 residues within 4Å: Chain B: R.192, R.257 Ligands: SO4.38 Ligand excluded by PLIP

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.20: 1 residues within 4Å: Chain A: R.267 No protein-ligand interaction detected (PLIP) GOL.21: 10 residues within 4Å: Chain A: G.51, F.52, R.55, Y.56, Q.144, Q.147, D.148, P.201, Y.213 Chain B: G.45 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.55, A:Q.144 GOL.22: 3 residues within 4Å: Chain A: H.245, Q.246, G.247 No protein-ligand interaction detected (PLIP) GOL.23: 3 residues within 4Å: Chain A: I.127, G.130, T.132 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.127, A:T.132 Water bridges: A:G.130, A:T.132, A:T.132 GOL.24: 9 residues within 4Å: Chain A: Q.37, H.139, N.184, Q.185, N.326, E.407, W.455, E.462, F.463 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.37, A:Q.37, A:N.184, A:Q.185, A:N.326, A:E.462 Water bridges: A:N.460 GOL.44: 1 residues within 4Å: Chain B: R.267 No protein-ligand interaction detected (PLIP) GOL.45: 10 residues within 4Å: Chain A: G.45 Chain B: G.51, F.52, R.55, Y.56, Q.144, Q.147, D.148, P.201, Y.213 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.55, B:Q.144 Water bridges: B:D.148 GOL.46: 3 residues within 4Å: Chain B: H.245, Q.246, G.247 No protein-ligand interaction detected (PLIP) GOL.47: 3 residues within 4Å: Chain B: I.127, G.130, T.132 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.127, B:T.132 Water bridges: B:G.130, B:T.132 GOL.48: 9 residues within 4Å: Chain B: Q.37, H.139, N.184, Q.185, N.326, E.407, W.455, E.462, F.463 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.37, B:Q.37, B:N.184, B:Q.185, B:N.326, B:E.462 Water bridges: B:N.460

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Burmeister, W.P., Structural Changes in a Cryo-Cooled Protein Crystal due to Radiation Damage. Acta Crystallogr.,Sect.D (2000)

Release Date

2000-03-03

Peptides

MYROSINASE MA1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
M

B
M

MYROSINASE MA1

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