SMTL ID : 8r7i.1

X-ray structure of blue laccase BP76 from the termite Neocapritermes taracua

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

NAG-NAG-BMA-MAN-NAG-FUC-FUC.1: 6 residues within 4Å: Chain A: A.54, C.55, G.56, N.61, A.64, A.67 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:A.67 Water bridges: A:P.53, A:G.56, B:N.424, B:N.427, B:N.427 NAG-NAG-BMA-MAN-NAG-FUC-FUC.20: 6 residues within 4Å: Chain B: A.54, C.55, G.56, N.61, A.64, A.67 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:A.67 Water bridges: B:P.53, B:G.56, A:N.424, A:N.427, A:N.427

2 x NAG- NAG- BMA- 01- NAG- MAN: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-3-O-sulfo-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-01-NAG-MAN.2: 13 residues within 4Å: Chain A: N.74, Y.76, N.206, R.219, L.220, I.226, T.236, L.238, I.244, G.245, D.337, E.338 Ligands: CL.16 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.338, A:D.337 Water bridges: A:S.335, A:D.337, A:D.337 NAG-NAG-BMA-01-NAG-MAN.21: 13 residues within 4Å: Chain B: N.74, Y.76, N.206, R.219, L.220, I.226, T.236, L.238, I.244, G.245, D.337, E.338 Ligands: CL.35 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.338 Water bridges: B:E.338, B:S.335, B:D.337, B:D.337, B:E.338

2 x NAG- NAG- BMA- 01- MAN- FUC- FUC: 3-O-sulfo-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)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-01-MAN-FUC-FUC.3: 11 residues within 4Å: Chain A: Q.375, N.376, P.515, A.516, S.517, D.518, Q.537, F.538, S.572, N.573 Ligands: CL.13 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Q.537, A:P.515 Hydrogen bonds: A:N.573, A:D.518 Water bridges: A:P.515, A:S.517, A:S.517 NAG-NAG-BMA-01-MAN-FUC-FUC.22: 11 residues within 4Å: Chain B: Q.375, N.376, P.515, A.516, S.517, D.518, Q.537, F.538, S.572, N.573 Ligands: CL.32 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Q.537, B:P.515 Hydrogen bonds: B:N.573, B:D.518 Water bridges: B:P.515, B:S.517, B:S.517

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

NAG-NAG.4: 2 residues within 4Å: Chain A: N.448, N.449 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 2 residues within 4Å: Chain B: N.448, N.449 No protein-ligand interaction detected (PLIP)

2 x YKK: 2-methyl-5-oxidanyl-cyclohexa-2,5-diene-1,4-dione(Non-covalent)

YKK.5: 13 residues within 4Å: Chain A: E.224, V.272, F.416, F.435, V.437, P.438, M.443, A.516, S.517, L.519, H.597 Ligands: PLQ.6, YMR.7 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.416, A:F.416, A:V.437, A:V.437, A:A.516, A:L.519 Hydrogen bonds: A:E.224, A:S.517 Water bridges: A:Q.223 YKK.24: 13 residues within 4Å: Chain B: E.224, V.272, F.416, F.435, V.437, P.438, M.443, A.516, S.517, L.519, H.597 Ligands: PLQ.25, YMR.26 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.416, B:F.416, B:V.437, B:V.437, B:A.516, B:L.519 Hydrogen bonds: B:S.517 Water bridges: B:Q.223

2 x PLQ: 1,4-benzoquinone(Non-covalent)

PLQ.6: 11 residues within 4Å: Chain A: V.272, F.416, F.435, V.437, P.438, A.516, S.517, L.519, H.597 Ligands: YKK.5, YMR.7 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.416, A:F.416, A:V.437, A:V.437, A:L.519 Hydrogen bonds: A:S.517 PLQ.25: 11 residues within 4Å: Chain B: V.272, F.416, F.435, V.437, P.438, A.516, S.517, L.519, H.597 Ligands: YKK.24, YMR.26 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.416, B:F.416, B:V.437, B:V.437, B:L.519 Hydrogen bonds: B:S.517

2 x YMR: 2-methylcyclohexa-2,5-diene-1,4-dione(Non-covalent)

YMR.7: 12 residues within 4Å: Chain A: V.272, F.416, F.435, V.437, P.438, M.443, A.516, S.517, L.519, H.597 Ligands: YKK.5, PLQ.6 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.416, A:F.416, A:V.437, A:V.437, A:A.516, A:L.519 Hydrogen bonds: A:S.517 YMR.26: 12 residues within 4Å: Chain B: V.272, F.416, F.435, V.437, P.438, M.443, A.516, S.517, L.519, H.597 Ligands: YKK.24, PLQ.25 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.416, B:F.416, B:V.437, B:V.437, B:A.516, B:L.519 Hydrogen bonds: B:S.517

2 x OH: HYDROXIDE ION(Non-covalent)

OH.8: 12 residues within 4Å: Chain A: H.116, H.118, H.160, H.162, H.524, H.526, H.591, H.593 Ligands: CU.9, CU.10, CU.11, CL.17 No protein-ligand interaction detected (PLIP) OH.27: 12 residues within 4Å: Chain B: H.116, H.118, H.160, H.162, H.524, H.526, H.591, H.593 Ligands: CU.28, CU.29, CU.30, CL.36 No protein-ligand interaction detected (PLIP)

8 x CU: COPPER (II) ION(Non-covalent)

CU.9: 5 residues within 4Å: Chain A: H.162, H.526, H.591 Ligands: OH.8, CL.17 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.162, A:H.526, A:H.591, OH.8 CU.10: 6 residues within 4Å: Chain A: H.116, H.118, H.524, H.526 Ligands: OH.8, CL.17 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.116, A:H.524, H2O.19 CU.11: 5 residues within 4Å: Chain A: H.118, H.160, H.593 Ligands: OH.8, CL.17 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.118, A:H.160, A:H.593, OH.8 CU.12: 5 residues within 4Å: Chain A: H.521, C.592, F.594, H.597, M.602 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.521, A:C.592, A:H.597 CU.28: 5 residues within 4Å: Chain B: H.162, H.526, H.591 Ligands: OH.27, CL.36 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:H.162, B:H.526, B:H.591, OH.27 CU.29: 6 residues within 4Å: Chain B: H.116, H.118, H.524, H.526 Ligands: OH.27, CL.36 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.116, B:H.524, H2O.58 CU.30: 5 residues within 4Å: Chain B: H.118, H.160, H.593 Ligands: OH.27, CL.36 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:H.118, B:H.160, B:H.593, OH.27 CU.31: 5 residues within 4Å: Chain B: H.521, C.592, F.594, H.597, M.602 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.521, B:C.592, B:H.597

10 x CL: CHLORIDE ION(Non-functional Binders)

CL.13: 2 residues within 4Å: Ligands: NAG-NAG-BMA-01-MAN-FUC-FUC.3, NAG-NAG-BMA-01-MAN-FUC-FUC.3 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain A: G.124, Q.126, P.585, P.615 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain A: I.12, S.91 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain A: I.205, N.206, R.212 Ligands: NAG-NAG-BMA-01-NAG-MAN.2 Ligand excluded by PLIP CL.17: 12 residues within 4Å: Chain A: H.116, H.118, H.160, H.162, H.524, H.526, H.591, H.593 Ligands: OH.8, CU.9, CU.10, CU.11 Ligand excluded by PLIP CL.32: 2 residues within 4Å: Ligands: NAG-NAG-BMA-01-MAN-FUC-FUC.22, NAG-NAG-BMA-01-MAN-FUC-FUC.22 Ligand excluded by PLIP CL.33: 4 residues within 4Å: Chain B: G.124, Q.126, P.585, P.615 Ligand excluded by PLIP CL.34: 2 residues within 4Å: Chain B: I.12, S.91 Ligand excluded by PLIP CL.35: 4 residues within 4Å: Chain B: I.205, N.206, R.212 Ligands: NAG-NAG-BMA-01-NAG-MAN.21 Ligand excluded by PLIP CL.36: 12 residues within 4Å: Chain B: H.116, H.118, H.160, H.162, H.524, H.526, H.591, H.593 Ligands: OH.27, CU.28, CU.29, CU.30 Ligand excluded by PLIP

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

SO4.18: 3 residues within 4Å: Chain A: R.355, N.356, E.357 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.356, A:E.357 Water bridges: A:R.355, A:R.355 Salt bridges: A:R.355 SO4.19: 3 residues within 4Å: Chain A: G.475, R.476, Q.481 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.476, A:Q.481, A:Q.481 Salt bridges: A:R.476 SO4.37: 3 residues within 4Å: Chain B: R.355, N.356, E.357 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.356, B:E.357 Water bridges: B:R.355, B:R.355 Salt bridges: B:R.355 SO4.38: 3 residues within 4Å: Chain B: G.475, R.476, Q.481 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.476, B:Q.481, B:Q.481 Salt bridges: B:R.476

Links

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Citation

Skerlova, J. et al., Crystal structure of blue laccase BP76, a unique termite suicidal defense weapon. Structure (2024)

Release Date

2024-08-28

Peptides

Laccase BP76: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Laccase BP76