SMTL ID : 6l8s.1

High resolution crystal structure of crustacean hemocyanin.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

hetero-2-2-2-mer

Ligands

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

CU.1: 7 residues within 4Å: Chain A: H.190, H.194, H.220, F.367 Ligands: CU.2, O.4, O.5 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Ligand interactions Metal complexes: A:H.190, A:H.194, A:H.220, O.4, O.5 CU.2: 7 residues within 4Å: Chain A: H.220, H.340, H.344, H.380 Ligands: CU.1, O.4, O.5 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Ligand interactions Metal complexes: A:H.340, A:H.344, A:H.380, O.4, O.5 CU.13: 7 residues within 4Å: Chain B: H.191, H.195, H.221, F.368 Ligands: CU.14, O.16, O.17 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Ligand interactions Metal complexes: B:H.191, B:H.195, B:H.221, O.16, O.17 CU.14: 7 residues within 4Å: Chain B: H.221, H.341, H.345, H.381 Ligands: CU.13, O.16, O.17 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Ligand interactions Metal complexes: B:H.341, B:H.345, B:H.381, O.16, O.17 CU.28: 7 residues within 4Å: Chain C: H.191, H.195, H.221, F.368 Ligands: CU.29, O.30, O.31 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Ligand interactions Metal complexes: C:H.191, C:H.195, C:H.221, O.30, O.31 CU.29: 7 residues within 4Å: Chain C: H.221, H.341, H.345, H.381 Ligands: CU.28, O.30, O.31 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Ligand interactions Metal complexes: C:H.341, C:H.345, C:H.381, O.30, O.31 CU.41: 7 residues within 4Å: Chain D: H.190, H.194, H.220, F.367 Ligands: CU.42, O.44, O.45 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Ligand interactions Metal complexes: D:H.190, D:H.194, D:H.220, O.44, O.45 CU.42: 7 residues within 4Å: Chain D: H.220, H.340, H.344, H.380 Ligands: CU.41, O.44, O.45 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Ligand interactions Metal complexes: D:H.340, D:H.344, D:H.380, O.44, O.45 CU.53: 7 residues within 4Å: Chain E: H.191, H.195, H.221, F.368 Ligands: CU.54, O.56, O.57 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Ligand interactions Metal complexes: E:H.191, E:H.195, E:H.221, O.56, O.57 CU.54: 7 residues within 4Å: Chain E: H.221, H.341, H.345, H.381 Ligands: CU.53, O.56, O.57 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Ligand interactions Metal complexes: E:H.341, E:H.345, E:H.381, O.56, O.57 CU.68: 7 residues within 4Å: Chain F: H.191, H.195, H.221, F.368 Ligands: CU.69, O.70, O.71 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Ligand interactions Metal complexes: F:H.191, F:H.195, F:H.221, O.70, O.71 CU.69: 7 residues within 4Å: Chain F: H.221, H.341, H.345, H.381 Ligands: CU.68, O.70, O.71 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Ligand interactions Metal complexes: F:H.341, F:H.345, F:H.381, O.70, O.71

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

NAG.3: 4 residues within 4Å: Chain A: N.163, E.424, R.447, H.449 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.163, A:E.424, A:R.447 NAG.15: 3 residues within 4Å: Chain B: N.164, E.425, R.448 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.164, B:E.425, B:R.448 NAG.43: 4 residues within 4Å: Chain D: N.163, E.424, R.447, H.449 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.163, D:E.424, D:R.447 NAG.55: 3 residues within 4Å: Chain E: N.164, E.425, R.448 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:N.164, E:E.425, E:R.448

12 x O: OXYGEN ATOM(Non-covalent)

O.4: 10 residues within 4Å: Chain A: H.190, H.194, H.220, H.340, H.344, F.367, H.380 Ligands: CU.1, CU.2, O.5 No protein-ligand interaction detected (PLIP) O.5: 10 residues within 4Å: Chain A: H.190, H.194, H.220, H.340, H.344, F.376, H.380 Ligands: CU.1, CU.2, O.4 No protein-ligand interaction detected (PLIP) O.16: 10 residues within 4Å: Chain B: H.191, H.195, H.221, H.341, H.345, F.368, H.381 Ligands: CU.13, CU.14, O.17 No protein-ligand interaction detected (PLIP) O.17: 10 residues within 4Å: Chain B: H.191, H.195, H.221, H.341, H.345, F.377, H.381 Ligands: CU.13, CU.14, O.16 No protein-ligand interaction detected (PLIP) O.30: 10 residues within 4Å: Chain C: H.191, H.195, H.221, H.341, H.345, F.377, H.381 Ligands: CU.28, CU.29, O.31 No protein-ligand interaction detected (PLIP) O.31: 9 residues within 4Å: Chain C: H.191, H.195, H.221, H.341, H.345, F.368 Ligands: CU.28, CU.29, O.30 No protein-ligand interaction detected (PLIP) O.44: 10 residues within 4Å: Chain D: H.190, H.194, H.220, H.340, H.344, F.367, H.380 Ligands: CU.41, CU.42, O.45 No protein-ligand interaction detected (PLIP) O.45: 10 residues within 4Å: Chain D: H.190, H.194, H.220, H.340, H.344, F.376, H.380 Ligands: CU.41, CU.42, O.44 No protein-ligand interaction detected (PLIP) O.56: 10 residues within 4Å: Chain E: H.191, H.195, H.221, H.341, H.345, F.368, H.381 Ligands: CU.53, CU.54, O.57 No protein-ligand interaction detected (PLIP) O.57: 10 residues within 4Å: Chain E: H.191, H.195, H.221, H.341, H.345, F.377, H.381 Ligands: CU.53, CU.54, O.56 No protein-ligand interaction detected (PLIP) O.70: 10 residues within 4Å: Chain F: H.191, H.195, H.221, H.341, H.345, F.377, H.381 Ligands: CU.68, CU.69, O.71 No protein-ligand interaction detected (PLIP) O.71: 9 residues within 4Å: Chain F: H.191, H.195, H.221, H.341, H.345, F.368 Ligands: CU.68, CU.69, O.70 No protein-ligand interaction detected (PLIP)

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

SO4.6: 5 residues within 4Å: Chain A: V.239, D.240, R.249, E.250, R.378 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.240 Water bridges: A:R.231, A:R.249, A:E.250 Salt bridges: A:R.249, A:R.378 SO4.18: 4 residues within 4Å: Chain B: V.240, D.241, R.250, R.379 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.241 Water bridges: B:R.232, B:R.250, B:E.251 Salt bridges: B:R.250, B:R.379 SO4.32: 5 residues within 4Å: Chain C: V.240, D.241, R.250, E.251, R.379 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.241 Water bridges: C:R.250, C:E.251 Salt bridges: C:R.250, C:R.379 SO4.46: 5 residues within 4Å: Chain D: V.239, D.240, R.249, E.250, R.378 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:D.240 Water bridges: D:R.231, D:R.249, D:E.250 Salt bridges: D:R.249, D:R.378 SO4.58: 4 residues within 4Å: Chain E: V.240, D.241, R.250, R.379 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:D.241 Water bridges: E:R.232, E:R.250, E:E.251 Salt bridges: E:R.250, E:R.379 SO4.72: 5 residues within 4Å: Chain F: V.240, D.241, R.250, E.251, R.379 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:D.241 Water bridges: F:R.250, F:E.251 Salt bridges: F:R.250, F:R.379

10 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 1 residues within 4Å: Chain A: H.66 No protein-ligand interaction detected (PLIP) MG.19: 2 residues within 4Å: Chain B: D.21, Q.65 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.21, H2O.20, H2O.24, H2O.30, H2O.31 MG.20: 2 residues within 4Å: Chain B: M.286, T.289 No protein-ligand interaction detected (PLIP) MG.33: 5 residues within 4Å: Chain C: H.400, R.631, V.632, G.635, V.636 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.400, C:V.632 MG.34: 4 residues within 4Å: Chain C: S.523, T.526, E.556, G.601 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:S.523, C:T.526, C:E.556, C:G.601, H2O.35 MG.47: 1 residues within 4Å: Chain D: H.66 No protein-ligand interaction detected (PLIP) MG.59: 2 residues within 4Å: Chain E: D.21, Q.65 5 PLIP interactions: 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:D.21, H2O.72, H2O.76, H2O.81, H2O.83 MG.60: 2 residues within 4Å: Chain E: M.286, T.289 No protein-ligand interaction detected (PLIP) MG.73: 5 residues within 4Å: Chain F: H.400, R.631, V.632, G.635, V.636 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:H.400, F:V.632 MG.74: 4 residues within 4Å: Chain F: S.523, T.526, E.556, G.601 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:S.523, F:T.526, F:E.556, F:G.601, H2O.86

34 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 8 residues within 4Å: Chain A: D.284, M.285, T.288, G.337, S.338, L.339, T.342 Ligands: EDO.38 Ligand excluded by PLIP EDO.9: 8 residues within 4Å: Chain A: P.265, V.266, R.267, L.347, G.348, Q.350, G.351, G.362 Ligand excluded by PLIP EDO.10: 10 residues within 4Å: Chain A: E.174, V.177, A.178, F.180, G.181, F.227, T.371, R.372, P.374, F.377 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: D.297, K.389 Chain B: D.285, I.288, T.289, R.292 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain A: K.503, F.504, F.505, R.517, S.523, G.599, H.602 Ligand excluded by PLIP EDO.21: 9 residues within 4Å: Chain B: E.175, V.178, A.179, F.181, G.182, F.228, T.372, R.373, P.375 Ligand excluded by PLIP EDO.22: 8 residues within 4Å: Chain B: P.266, V.267, R.268, L.348, G.349, Q.351, G.352, G.363 Ligand excluded by PLIP EDO.23: 9 residues within 4Å: Chain B: K.521, D.522, S.523, T.526, V.527, P.528, E.556, E.563, G.601 Ligand excluded by PLIP EDO.24: 9 residues within 4Å: Chain B: D.298, K.390 Chain C: T.289, R.292, Q.335, Y.336, G.338 Ligands: EDO.25, EDO.36 Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain B: Y.294, D.298, K.390 Chain C: D.285 Ligands: EDO.24 Ligand excluded by PLIP EDO.26: 6 residues within 4Å: Chain B: K.504, F.505, F.506, R.518, S.524, H.603 Ligand excluded by PLIP EDO.35: 8 residues within 4Å: Chain C: P.266, V.267, R.268, L.348, G.349, Q.351, G.352, G.363 Ligand excluded by PLIP EDO.36: 7 residues within 4Å: Chain C: D.285, M.286, T.289, G.338, S.339, T.343 Ligands: EDO.24 Ligand excluded by PLIP EDO.37: 9 residues within 4Å: Chain C: E.175, V.178, A.179, F.181, G.182, F.228, T.372, R.373, P.375 Ligand excluded by PLIP EDO.38: 9 residues within 4Å: Chain A: T.288, R.291, Q.334, Y.335, G.337 Chain C: D.298, K.390 Ligands: EDO.8, EDO.39 Ligand excluded by PLIP EDO.39: 4 residues within 4Å: Chain A: D.284 Chain C: Y.294, K.390 Ligands: EDO.38 Ligand excluded by PLIP EDO.40: 7 residues within 4Å: Chain C: K.504, F.505, F.506, R.518, D.522, S.524, H.603 Ligand excluded by PLIP EDO.48: 8 residues within 4Å: Chain D: D.284, M.285, T.288, G.337, S.338, L.339, T.342 Ligands: EDO.78 Ligand excluded by PLIP EDO.49: 8 residues within 4Å: Chain D: P.265, V.266, R.267, L.347, G.348, Q.350, G.351, G.362 Ligand excluded by PLIP EDO.50: 10 residues within 4Å: Chain D: E.174, V.177, A.178, F.180, G.181, F.227, T.371, R.372, P.374, F.377 Ligand excluded by PLIP EDO.51: 6 residues within 4Å: Chain D: D.297, K.389 Chain E: D.285, I.288, T.289, R.292 Ligand excluded by PLIP EDO.52: 7 residues within 4Å: Chain D: K.503, F.504, F.505, R.517, S.523, G.599, H.602 Ligand excluded by PLIP EDO.61: 9 residues within 4Å: Chain E: E.175, V.178, A.179, F.181, G.182, F.228, T.372, R.373, P.375 Ligand excluded by PLIP EDO.62: 8 residues within 4Å: Chain E: P.266, V.267, R.268, L.348, G.349, Q.351, G.352, G.363 Ligand excluded by PLIP EDO.63: 9 residues within 4Å: Chain E: K.521, D.522, S.523, T.526, V.527, P.528, E.556, E.563, G.601 Ligand excluded by PLIP EDO.64: 9 residues within 4Å: Chain E: D.298, K.390 Chain F: T.289, R.292, Q.335, Y.336, G.338 Ligands: EDO.65, EDO.76 Ligand excluded by PLIP EDO.65: 5 residues within 4Å: Chain E: Y.294, D.298, K.390 Chain F: D.285 Ligands: EDO.64 Ligand excluded by PLIP EDO.66: 6 residues within 4Å: Chain E: K.504, F.505, F.506, R.518, S.524, H.603 Ligand excluded by PLIP EDO.75: 8 residues within 4Å: Chain F: P.266, V.267, R.268, L.348, G.349, Q.351, G.352, G.363 Ligand excluded by PLIP EDO.76: 7 residues within 4Å: Chain F: D.285, M.286, T.289, G.338, S.339, T.343 Ligands: EDO.64 Ligand excluded by PLIP EDO.77: 9 residues within 4Å: Chain F: E.175, V.178, A.179, F.181, G.182, F.228, T.372, R.373, P.375 Ligand excluded by PLIP EDO.78: 9 residues within 4Å: Chain D: T.288, R.291, Q.334, Y.335, G.337 Chain F: D.298, K.390 Ligands: EDO.48, EDO.79 Ligand excluded by PLIP EDO.79: 4 residues within 4Å: Chain D: D.284 Chain F: Y.294, K.390 Ligands: EDO.78 Ligand excluded by PLIP EDO.80: 7 residues within 4Å: Chain F: K.504, F.505, F.506, R.518, D.522, S.524, H.603 Ligand excluded by PLIP

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

CL.27: 2 residues within 4Å: Chain B: H.514, T.515 Ligand excluded by PLIP CL.67: 2 residues within 4Å: Chain E: H.514, T.515 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Masuda, T. et al., The high-resolution crystal structure of lobster hemocyanin shows its enzymatic capability as a phenoloxidase. Arch.Biochem.Biophys. (2020)

Release Date

2020-05-27

Peptides

Hemocyanin: AD
Hemocyanin: BE
Hemocyanin: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

B
B

E
B

C
C

F
C

Hemocyanin

Hemocyanin

Hemocyanin