SMTL ID : 5nqo.1

CU(I)-CSP3 (COPPER STORAGE PROTEIN 3) FROM METHYLOSINUS

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.15 Å

Oligo State

homo-tetramer

Ligands

68 x CU1: COPPER (I) ION(Non-covalent)

CU1.1: 7 residues within 4Å: Chain A: C.28, C.90, C.121, C.125 Ligands: CU1.2, CU1.3, CU1.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.90, A:C.125 CU1.2: 6 residues within 4Å: Chain A: C.28, C.121, E.122, C.125 Ligands: CU1.1, CU1.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.121, A:C.121, A:C.125 CU1.3: 11 residues within 4Å: Chain A: C.28, C.31, C.65, C.90, C.94, C.121 Ligands: CU1.1, CU1.2, CU1.4, CU1.5, CU1.6 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.65, A:C.121 CU1.4: 8 residues within 4Å: Chain A: C.65, C.90, A.91, C.94 Ligands: CU1.1, CU1.3, CU1.5, CU1.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.90, A:C.90, A:C.94 CU1.5: 10 residues within 4Å: Chain A: C.31, C.61, C.65, C.94, C.121 Ligands: CU1.3, CU1.4, CU1.6, CU1.7, CU1.8 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.31, A:C.94 CU1.6: 8 residues within 4Å: Chain A: C.61, C.65, C.94 Ligands: CU1.3, CU1.4, CU1.5, CU1.7, CU1.8 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.61, A:C.61, A:C.65 CU1.7: 10 residues within 4Å: Chain A: C.31, C.35, C.61, C.97, C.118 Ligands: CU1.5, CU1.6, CU1.8, CU1.9, CU1.10 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.35, A:C.61, A:C.118 CU1.8: 9 residues within 4Å: Chain A: C.31, A.32, C.35, C.118 Ligands: CU1.5, CU1.6, CU1.7, CU1.9, CU1.10 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.31, A:C.31, A:C.35 CU1.9: 11 residues within 4Å: Chain A: C.35, N.58, C.61, C.97, C.114, C.118 Ligands: CU1.7, CU1.8, CU1.10, CU1.11, CU1.12 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.35, A:C.97 CU1.10: 8 residues within 4Å: Chain A: C.35, C.114, A.115, C.118 Ligands: CU1.7, CU1.8, CU1.9, CU1.11 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.114, A:C.114, A:C.118 CU1.11: 9 residues within 4Å: Chain A: C.38, N.58, C.97, C.101, C.114 Ligands: CU1.9, CU1.10, CU1.12, CU1.13 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.101, A:C.114 CU1.12: 6 residues within 4Å: Chain A: N.58, C.97, E.98, C.101 Ligands: CU1.9, CU1.11 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.97, A:C.97, A:C.101 CU1.13: 11 residues within 4Å: Chain A: C.38, C.54, N.58, C.101, C.111, C.114 Ligands: CU1.11, CU1.14, CU1.15, CU1.16, CU1.17 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.38, A:C.101, A:C.111 CU1.14: 10 residues within 4Å: Chain A: C.38, A.39, C.42, N.58, H.110, C.111 Ligands: CU1.13, CU1.15, CU1.16, CU1.17 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.38, A:C.38, A:C.42 CU1.15: 8 residues within 4Å: Chain A: C.42, C.54, N.58, C.111 Ligands: CU1.13, CU1.14, CU1.16, CU1.17 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.42, A:C.54 CU1.16: 9 residues within 4Å: Chain A: C.38, C.42, H.108, H.110, C.111 Ligands: CU1.13, CU1.14, CU1.15, CU1.17 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.110, A:C.111 CU1.17: 10 residues within 4Å: Chain A: C.38, C.42, C.54, C.101, H.104, C.111 Ligands: CU1.13, CU1.14, CU1.15, CU1.16 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.54, A:C.111 CU1.19: 7 residues within 4Å: Chain B: C.28, C.90, C.121, C.125 Ligands: CU1.20, CU1.21, CU1.22 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.90, B:C.125 CU1.20: 6 residues within 4Å: Chain B: C.28, C.121, E.122, C.125 Ligands: CU1.19, CU1.21 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.121, B:C.121, B:C.125 CU1.21: 11 residues within 4Å: Chain B: C.28, C.31, C.65, C.90, C.94, C.121 Ligands: CU1.19, CU1.20, CU1.22, CU1.23, CU1.24 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.65, B:C.121 CU1.22: 8 residues within 4Å: Chain B: C.65, C.90, A.91, C.94 Ligands: CU1.19, CU1.21, CU1.23, CU1.24 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.90, B:C.90, B:C.94 CU1.23: 10 residues within 4Å: Chain B: C.31, C.61, C.65, C.94, C.121 Ligands: CU1.21, CU1.22, CU1.24, CU1.25, CU1.26 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.31, B:C.94 CU1.24: 8 residues within 4Å: Chain B: C.61, C.65, C.94 Ligands: CU1.21, CU1.22, CU1.23, CU1.25, CU1.26 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.61, B:C.61, B:C.65 CU1.25: 10 residues within 4Å: Chain B: C.31, C.35, C.61, C.97, C.118 Ligands: CU1.23, CU1.24, CU1.26, CU1.27, CU1.28 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.35, B:C.61, B:C.118 CU1.26: 9 residues within 4Å: Chain B: C.31, A.32, C.35, C.118 Ligands: CU1.23, CU1.24, CU1.25, CU1.27, CU1.28 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.31, B:C.31, B:C.35 CU1.27: 11 residues within 4Å: Chain B: C.35, N.58, C.61, C.97, C.114, C.118 Ligands: CU1.25, CU1.26, CU1.28, CU1.29, CU1.30 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.35, B:C.97 CU1.28: 8 residues within 4Å: Chain B: C.35, C.114, A.115, C.118 Ligands: CU1.25, CU1.26, CU1.27, CU1.29 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.114, B:C.114, B:C.118 CU1.29: 9 residues within 4Å: Chain B: C.38, N.58, C.97, C.101, C.114 Ligands: CU1.27, CU1.28, CU1.30, CU1.31 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.101, B:C.114 CU1.30: 6 residues within 4Å: Chain B: N.58, C.97, E.98, C.101 Ligands: CU1.27, CU1.29 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.97, B:C.97, B:C.101 CU1.31: 11 residues within 4Å: Chain B: C.38, C.54, N.58, C.101, C.111, C.114 Ligands: CU1.29, CU1.32, CU1.33, CU1.34, CU1.35 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.38, B:C.101, B:C.111 CU1.32: 10 residues within 4Å: Chain B: C.38, A.39, C.42, N.58, H.110, C.111 Ligands: CU1.31, CU1.33, CU1.34, CU1.35 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.38, B:C.38, B:C.42 CU1.33: 8 residues within 4Å: Chain B: C.42, C.54, N.58, C.111 Ligands: CU1.31, CU1.32, CU1.34, CU1.35 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.42, B:C.54 CU1.34: 9 residues within 4Å: Chain B: C.38, C.42, H.108, H.110, C.111 Ligands: CU1.31, CU1.32, CU1.33, CU1.35 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.110, B:C.111 CU1.35: 10 residues within 4Å: Chain B: C.38, C.42, C.54, C.101, H.104, C.111 Ligands: CU1.31, CU1.32, CU1.33, CU1.34 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.54, B:C.111 CU1.37: 7 residues within 4Å: Chain C: C.28, C.90, C.121, C.125 Ligands: CU1.38, CU1.39, CU1.40 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:C.90, C:C.125 CU1.38: 6 residues within 4Å: Chain C: C.28, C.121, E.122, C.125 Ligands: CU1.37, CU1.39 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.121, C:C.121, C:C.125 CU1.39: 11 residues within 4Å: Chain C: C.28, C.31, C.65, C.90, C.94, C.121 Ligands: CU1.37, CU1.38, CU1.40, CU1.41, CU1.42 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:C.65, C:C.121 CU1.40: 8 residues within 4Å: Chain C: C.65, C.90, A.91, C.94 Ligands: CU1.37, CU1.39, CU1.41, CU1.42 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.90, C:C.90, C:C.94 CU1.41: 10 residues within 4Å: Chain C: C.31, C.61, C.65, C.94, C.121 Ligands: CU1.39, CU1.40, CU1.42, CU1.43, CU1.44 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:C.31, C:C.94 CU1.42: 8 residues within 4Å: Chain C: C.61, C.65, C.94 Ligands: CU1.39, CU1.40, CU1.41, CU1.43, CU1.44 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.61, C:C.61, C:C.65 CU1.43: 10 residues within 4Å: Chain C: C.31, C.35, C.61, C.97, C.118 Ligands: CU1.41, CU1.42, CU1.44, CU1.45, CU1.46 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.35, C:C.61, C:C.118 CU1.44: 9 residues within 4Å: Chain C: C.31, A.32, C.35, C.118 Ligands: CU1.41, CU1.42, CU1.43, CU1.45, CU1.46 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.31, C:C.31, C:C.35 CU1.45: 11 residues within 4Å: Chain C: C.35, N.58, C.61, C.97, C.114, C.118 Ligands: CU1.43, CU1.44, CU1.46, CU1.47, CU1.48 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:C.35, C:C.97 CU1.46: 8 residues within 4Å: Chain C: C.35, C.114, A.115, C.118 Ligands: CU1.43, CU1.44, CU1.45, CU1.47 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.114, C:C.114, C:C.118 CU1.47: 9 residues within 4Å: Chain C: C.38, N.58, C.97, C.101, C.114 Ligands: CU1.45, CU1.46, CU1.48, CU1.49 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:C.101, C:C.114 CU1.48: 6 residues within 4Å: Chain C: N.58, C.97, E.98, C.101 Ligands: CU1.45, CU1.47 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.97, C:C.97, C:C.101 CU1.49: 11 residues within 4Å: Chain C: C.38, C.54, N.58, C.101, C.111, C.114 Ligands: CU1.47, CU1.50, CU1.51, CU1.52, CU1.53 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.38, C:C.101, C:C.111 CU1.50: 10 residues within 4Å: Chain C: C.38, A.39, C.42, N.58, H.110, C.111 Ligands: CU1.49, CU1.51, CU1.52, CU1.53 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.38, C:C.38, C:C.42 CU1.51: 8 residues within 4Å: Chain C: C.42, C.54, N.58, C.111 Ligands: CU1.49, CU1.50, CU1.52, CU1.53 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:C.42, C:C.54 CU1.52: 9 residues within 4Å: Chain C: C.38, C.42, H.108, H.110, C.111 Ligands: CU1.49, CU1.50, CU1.51, CU1.53 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.110, C:C.111 CU1.53: 10 residues within 4Å: Chain C: C.38, C.42, C.54, C.101, H.104, C.111 Ligands: CU1.49, CU1.50, CU1.51, CU1.52 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:C.54, C:C.111 CU1.55: 7 residues within 4Å: Chain D: C.28, C.90, C.121, C.125 Ligands: CU1.56, CU1.57, CU1.58 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:C.90, D:C.125 CU1.56: 6 residues within 4Å: Chain D: C.28, C.121, E.122, C.125 Ligands: CU1.55, CU1.57 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.121, D:C.121, D:C.125 CU1.57: 11 residues within 4Å: Chain D: C.28, C.31, C.65, C.90, C.94, C.121 Ligands: CU1.55, CU1.56, CU1.58, CU1.59, CU1.60 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:C.65, D:C.121 CU1.58: 8 residues within 4Å: Chain D: C.65, C.90, A.91, C.94 Ligands: CU1.55, CU1.57, CU1.59, CU1.60 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.90, D:C.90, D:C.94 CU1.59: 10 residues within 4Å: Chain D: C.31, C.61, C.65, C.94, C.121 Ligands: CU1.57, CU1.58, CU1.60, CU1.61, CU1.62 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:C.31, D:C.94 CU1.60: 8 residues within 4Å: Chain D: C.61, C.65, C.94 Ligands: CU1.57, CU1.58, CU1.59, CU1.61, CU1.62 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.61, D:C.61, D:C.65 CU1.61: 10 residues within 4Å: Chain D: C.31, C.35, C.61, C.97, C.118 Ligands: CU1.59, CU1.60, CU1.62, CU1.63, CU1.64 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.35, D:C.61, D:C.118 CU1.62: 9 residues within 4Å: Chain D: C.31, A.32, C.35, C.118 Ligands: CU1.59, CU1.60, CU1.61, CU1.63, CU1.64 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.31, D:C.31, D:C.35 CU1.63: 11 residues within 4Å: Chain D: C.35, N.58, C.61, C.97, C.114, C.118 Ligands: CU1.61, CU1.62, CU1.64, CU1.65, CU1.66 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:C.35, D:C.97 CU1.64: 8 residues within 4Å: Chain D: C.35, C.114, A.115, C.118 Ligands: CU1.61, CU1.62, CU1.63, CU1.65 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.114, D:C.114, D:C.118 CU1.65: 9 residues within 4Å: Chain D: C.38, N.58, C.97, C.101, C.114 Ligands: CU1.63, CU1.64, CU1.66, CU1.67 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:C.101, D:C.114 CU1.66: 6 residues within 4Å: Chain D: N.58, C.97, E.98, C.101 Ligands: CU1.63, CU1.65 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.97, D:C.97, D:C.101 CU1.67: 11 residues within 4Å: Chain D: C.38, C.54, N.58, C.101, C.111, C.114 Ligands: CU1.65, CU1.68, CU1.69, CU1.70, CU1.71 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.38, D:C.101, D:C.111 CU1.68: 10 residues within 4Å: Chain D: C.38, A.39, C.42, N.58, H.110, C.111 Ligands: CU1.67, CU1.69, CU1.70, CU1.71 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.38, D:C.38, D:C.42 CU1.69: 8 residues within 4Å: Chain D: C.42, C.54, N.58, C.111 Ligands: CU1.67, CU1.68, CU1.70, CU1.71 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:C.42, D:C.54 CU1.70: 9 residues within 4Å: Chain D: C.38, C.42, H.108, H.110, C.111 Ligands: CU1.67, CU1.68, CU1.69, CU1.71 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:H.110, D:C.111 CU1.71: 10 residues within 4Å: Chain D: C.38, C.42, C.54, C.101, H.104, C.111 Ligands: CU1.67, CU1.68, CU1.69, CU1.70 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:C.54, D:C.111

4 x NA: SODIUM ION(Non-functional Binders)

NA.18: 2 residues within 4Å: Chain A: R.74, E.79 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.74 NA.36: 2 residues within 4Å: Chain B: R.74, E.79 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.74 NA.54: 2 residues within 4Å: Chain C: R.74, E.79 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.79 NA.72: 2 residues within 4Å: Chain D: R.74, E.79 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.79, D:E.79

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Basle, A. et al., Visualizing Biological Copper Storage: The Importance of Thiolate-Coordinated Tetranuclear Clusters. Angew. Chem. Int. Ed. Engl. (2017)

Release Date

2017-05-31

Peptides

CSP3: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

CSP3

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