SMTL ID : 5g3b.1

Preserving metallic sites affected by radiation damage: the CuT2 case in Thermus thermophilus multicopper oxidase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

homo-dimer

Ligands

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

MPD.1: 4 residues within 4Å: Chain A: E.104, L.105, F.228, S.311 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.311, A:S.311 Water bridges: A:K.103, A:E.104, A:S.135, A:S.136 MPD.2: 6 residues within 4Å: Chain A: L.233, V.235, E.237, L.238, P.390 Ligands: MPD.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.235, A:L.238 Water bridges: A:E.237 MPD.3: 7 residues within 4Å: Chain A: P.168, W.171, M.332, A.333, R.430 Ligands: MRD.7, MRD.14 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.168, A:W.171 Hydrogen bonds: A:A.333 Water bridges: A:W.171, A:R.430 MPD.6: 13 residues within 4Å: Chain A: L.221, A.224, D.225, L.238, L.239, L.240, E.244, R.245, A.246, F.389, Y.391, K.395 Ligands: MPD.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.224, A:L.240, A:A.246, A:F.389, A:K.395 Hydrogen bonds: A:R.245, A:Y.391 MPD.11: 6 residues within 4Å: Chain A: D.216, H.217, P.218, S.236 Chain B: R.253 Ligands: MRD.20 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.216 Water bridges: A:D.216, A:H.217, A:S.236 MPD.16: 4 residues within 4Å: Chain B: E.104, L.105, F.228, S.311 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.311, B:S.311 Water bridges: B:K.103, B:E.104, B:S.135, B:S.136 MPD.17: 6 residues within 4Å: Chain B: L.233, V.235, E.237, L.238, P.390 Ligands: MPD.21 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.235, B:L.238 Water bridges: B:E.237 MPD.18: 7 residues within 4Å: Chain B: P.168, W.171, M.332, A.333, R.430 Ligands: MRD.22, MRD.29 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:P.168, B:W.171 Hydrogen bonds: B:A.333 Water bridges: B:W.171, B:R.430 MPD.21: 13 residues within 4Å: Chain B: L.221, A.224, D.225, L.238, L.239, L.240, E.244, R.245, A.246, F.389, Y.391, K.395 Ligands: MPD.17 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.224, B:L.240, B:A.246, B:F.389, B:K.395 Hydrogen bonds: B:R.245 MPD.26: 6 residues within 4Å: Chain A: R.253 Chain B: D.216, H.217, P.218, S.236 Ligands: MRD.5 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.216 Water bridges: B:D.216, B:D.216, B:H.217, B:S.236

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

MRD.4: 4 residues within 4Å: Chain A: P.2, S.3, V.191, Q.193 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.191, A:V.191 Hydrogen bonds: A:S.3 Water bridges: A:F.4 MRD.5: 5 residues within 4Å: Chain A: R.253, P.303 Chain B: P.218, E.234 Ligands: MPD.26 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.218, B:E.234, A:R.253 MRD.7: 5 residues within 4Å: Chain A: G.117, W.171, D.429, R.430 Ligands: MPD.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.117 MRD.12: 5 residues within 4Å: Chain A: E.104, L.316, W.394, P.411, R.413 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.104, A:P.411 MRD.13: 2 residues within 4Å: Chain A: K.415, G.416 No protein-ligand interaction detected (PLIP) MRD.14: 4 residues within 4Å: Chain A: P.168, M.272, M.332 Ligands: MPD.3 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.168 MRD.19: 4 residues within 4Å: Chain B: P.2, S.3, V.191, Q.193 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.191, B:V.191 Hydrogen bonds: B:S.3 Water bridges: B:F.4 MRD.20: 5 residues within 4Å: Chain A: P.218, E.234 Chain B: R.253, P.303 Ligands: MPD.11 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.218, A:E.234, B:R.253 MRD.22: 5 residues within 4Å: Chain B: G.117, W.171, D.429, R.430 Ligands: MPD.18 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.117 MRD.27: 5 residues within 4Å: Chain B: E.104, L.316, W.394, 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.28: 2 residues within 4Å: Chain B: K.415, G.416 No protein-ligand interaction detected (PLIP) MRD.29: 4 residues within 4Å: Chain B: P.168, M.272, M.332 Ligands: MPD.18 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.168

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

CU.8: 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.9: 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.10: 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.23: 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.24: 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.25: 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

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

NA.15: 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:S.22, A:S.22 NA.30: 3 residues within 4Å: Chain B: T.24, G.42, R.64 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.24, B:T.24, B:R.64 Water bridges: B:S.22

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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