SMTL ID : 5g3e.1

Preserving Metallic Sites Affected by Radiation DAmage the CuT2 CAse in THermus Thermophilus Multicopper Oxidase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

homo-dimer

Ligands

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

CU.1: 5 residues within 4Å: Chain A: H.72, H.114, H.373, H.375, H.421 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.114, A:H.375, A:H.421 CU.2: 5 residues within 4Å: Chain A: H.370, C.422, I.424, H.427, M.432 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.370, A:C.422, A:H.427 CU.3: 5 residues within 4Å: Chain A: H.72, H.74, W.110, H.112, H.423 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.74, A:H.112, A:H.423 CU.15: 5 residues within 4Å: Chain B: H.72, H.114, H.373, H.375, H.421 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.114, B:H.375, B:H.421 CU.16: 5 residues within 4Å: Chain B: H.370, C.422, I.424, H.427, M.432 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.370, B:C.422, B:H.427 CU.17: 5 residues within 4Å: Chain B: H.72, H.74, W.110, H.112, H.423 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.74, B:H.112, B:H.423

12 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.4: 4 residues within 4Å: Chain A: G.117, W.171, D.429, R.430 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.171 Hydrogen bonds: A:D.429 MPD.6: 5 residues within 4Å: Chain A: P.168, M.169, M.272, M.331, M.332 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.168 Hydrogen bonds: A:P.168 MPD.7: 11 residues within 4Å: Chain A: L.221, A.224, D.225, L.238, L.239, L.240, E.244, R.245, A.246, Y.391, K.395 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.224, A:L.240, A:K.395 Hydrogen bonds: A:R.245, A:Y.391 MPD.9: 6 residues within 4Å: Chain A: D.216, H.217, P.218, S.236 Chain B: R.253 Ligands: MRD.24 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.216, A:D.216 Water bridges: A:H.217 MPD.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MPD.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MPD.18: 4 residues within 4Å: Chain B: G.117, W.171, D.429, R.430 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.171 Hydrogen bonds: B:D.429 MPD.20: 5 residues within 4Å: Chain B: P.168, M.169, M.272, M.331, M.332 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.168 Hydrogen bonds: B:P.168 MPD.21: 11 residues within 4Å: Chain B: L.221, A.224, D.225, L.238, L.239, L.240, E.244, R.245, A.246, Y.391, K.395 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:A.224, B:L.240, B:K.395 Hydrogen bonds: B:R.245 MPD.23: 6 residues within 4Å: Chain A: R.253 Chain B: D.216, H.217, P.218, S.236 Ligands: MRD.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.216, B:D.216 Water bridges: B:H.217 MPD.26: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MPD.27: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

8 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.5: 4 residues within 4Å: Chain A: E.104, L.316, P.411, R.413 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.104, A:P.411 MRD.8: 7 residues within 4Å: Chain A: E.104, L.105, A.106, S.135, S.136, F.228, S.311 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.135, A:S.311, A:S.311 MRD.10: 7 residues within 4Å: Chain A: R.251, R.253, P.303 Chain B: E.234, V.235, S.236 Ligands: MPD.23 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:R.253, A:P.303 Hydrogen bonds: A:R.251, B:E.234, B:E.234 MRD.11: 4 residues within 4Å: Chain A: P.2, S.3, V.191, Q.193 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:P.2, A:V.191 Hydrogen bonds: A:S.3 Water bridges: A:S.3, A:F.4, A:F.4, A:V.191, A:V.191, A:Q.193 MRD.19: 4 residues within 4Å: Chain B: E.104, L.316, P.411, R.413 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:E.104, B:P.411 Water bridges: B:E.104 MRD.22: 7 residues within 4Å: Chain B: E.104, L.105, A.106, S.135, S.136, F.228, S.311 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.135, B:S.311, B:S.311 MRD.24: 7 residues within 4Å: Chain A: E.234, V.235, S.236 Chain B: R.251, R.253, P.303 Ligands: MPD.9 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:R.253, B:P.303 Hydrogen bonds: B:R.251, A:E.234 MRD.25: 4 residues within 4Å: Chain B: P.2, S.3, V.191, Q.193 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:P.2, B:V.191 Hydrogen bonds: B:S.3 Water bridges: B:S.3, B:F.4, B:F.4, B:V.191, B:V.191, B:Q.193

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

NA.14: 3 residues within 4Å: Chain A: T.24, G.42, R.64 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.64 Water bridges: A:T.24, A:G.42 NA.28: 3 residues within 4Å: Chain B: T.24, G.42, R.64 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.24, B:R.64 Water bridges: B:G.42

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ruiz-Arellano, R. et al., Preserving Metallic Sites Affected by Radiation Damage the Cut2 Case in Thermus Thermophilus Multicopper Oxidase. To be Published

Release Date

2017-05-24

Peptides

THERMUS THERMOPHILUS MULTICOPPER OXIDASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

THERMUS THERMOPHILUS MULTICOPPER OXIDASE

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