SMTL ID : 5g3d.1

preserving Metallic Sites Affected by Radiation Damage the CuT2 cCase 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.16: 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.17: 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.18: 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: 6 residues within 4Å: Chain A: E.104, L.105, A.106, S.135, F.228, S.311 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.106, A:F.228 Hydrogen bonds: A:E.104, A:E.104 MPD.6: 6 residues within 4Å: Chain A: D.216, H.217, P.218, S.236 Chain B: R.253 Ligands: MPD.23 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.218 Hydrogen bonds: A:S.236, B:R.253 Water bridges: A:D.216 MPD.7: 5 residues within 4Å: Chain A: K.8, L.19, L.21, G.41, P.47 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.8, A:L.19, A:L.21 Hydrogen bonds: A:K.8 MPD.8: 5 residues within 4Å: Chain A: R.251, R.253 Chain B: P.218, E.234 Ligands: MPD.21 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.253 Water bridges: A:R.251, A:R.251, B:R.253 Hydrophobic interactions: B:P.218 MPD.9: 1 residues within 4Å: Chain A: K.415 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:K.415 MPD.13: 11 residues within 4Å: Chain A: L.221, A.224, D.225, L.239, L.240, E.244, R.245, A.246, Y.391, K.395 Ligands: MRD.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.221, A:L.240, A:A.246 Hydrogen bonds: A:D.225, A:R.245, A:K.395 MPD.19: 6 residues within 4Å: Chain B: E.104, L.105, A.106, S.135, F.228, S.311 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.106, B:F.228 Hydrogen bonds: B:E.104 MPD.21: 6 residues within 4Å: Chain A: R.253 Chain B: D.216, H.217, P.218, S.236 Ligands: MPD.8 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.253, B:S.236 Hydrophobic interactions: B:P.218 Water bridges: B:D.216 MPD.22: 5 residues within 4Å: Chain B: K.8, L.19, L.21, G.41, P.47 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:K.8, B:L.19, B:L.21 Hydrogen bonds: B:K.8 MPD.23: 5 residues within 4Å: Chain A: P.218, E.234 Chain B: R.251, R.253 Ligands: MPD.6 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:P.218 Water bridges: A:R.253, B:R.251, B:R.251 Hydrogen bonds: B:R.253 MPD.24: 1 residues within 4Å: Chain B: K.415 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:K.415 MPD.28: 11 residues within 4Å: Chain B: L.221, A.224, D.225, L.239, L.240, E.244, R.245, A.246, Y.391, K.395 Ligands: MRD.20 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.221, B:L.240, B:A.246 Hydrogen bonds: B:D.225, B:R.245, B:Y.391, B:K.395

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

MRD.5: 6 residues within 4Å: Chain A: L.233, V.235, E.237, L.238, P.390 Ligands: MPD.13 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.238, A:P.390 MRD.10: 7 residues within 4Å: Chain A: P.168, M.169, M.172, M.272, M.331, M.332 Ligands: MRD.12 No protein-ligand interaction detected (PLIP) MRD.11: 6 residues within 4Å: Chain A: E.104, P.314, L.316, W.394, P.411, R.413 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:E.104, A:P.314, A:L.316, A:W.394, A:P.411 Water bridges: A:E.104 MRD.12: 7 residues within 4Å: Chain A: P.168, W.171, A.333, A.334, R.430 Ligands: MRD.10, MRD.14 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.168, A:P.168, A:W.171 Hydrogen bonds: A:A.333 Water bridges: A:R.430 MRD.14: 5 residues within 4Å: Chain A: G.117, W.171, D.429, R.430 Ligands: MRD.12 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.171, A:W.171, A:D.429 Hydrogen bonds: A:R.430 Water bridges: A:R.335, A:D.429 MRD.20: 6 residues within 4Å: Chain B: L.233, V.235, E.237, L.238, P.390 Ligands: MPD.28 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.238, B:P.390 MRD.25: 7 residues within 4Å: Chain B: P.168, M.169, M.172, M.272, M.331, M.332 Ligands: MRD.27 No protein-ligand interaction detected (PLIP) MRD.26: 6 residues within 4Å: Chain B: E.104, P.314, L.316, W.394, P.411, R.413 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:E.104, B:P.314, B:L.316, B:W.394, B:P.411 MRD.27: 7 residues within 4Å: Chain B: P.168, W.171, A.333, A.334, R.430 Ligands: MRD.25, MRD.29 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:P.168, B:P.168, B:W.171 Hydrogen bonds: B:A.333 Water bridges: B:R.430 MRD.29: 5 residues within 4Å: Chain B: G.117, W.171, D.429, R.430 Ligands: MRD.27 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.171, B:W.171, B:D.429 Hydrogen bonds: B:R.430 Water bridges: B:R.335, B:D.429

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

NA.15: 3 residues within 4Å: Chain A: T.24, G.42, R.64 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.24, A:T.24, A:R.64 Water bridges: A:G.42 NA.30: 3 residues within 4Å: Chain B: T.24, G.42, R.64 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.64 Water bridges: B:G.41, 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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