SMTL ID : 5k7a.1

Crystal structure of laccase fron Thermus thermophilus HB27 (sodium nitrate 1.5 min)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

3 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.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.3: 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

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

MPD.4: 4 residues within 4Å: Chain A: P.319, V.320, V.321, T.322 No protein-ligand interaction detected (PLIP) MPD.5: 5 residues within 4Å: Chain A: D.216, H.217, P.218, S.236 Ligands: MPD.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.216 Water bridges: A:D.216 MPD.6: 12 residues within 4Å: Chain A: L.221, A.224, D.225, L.239, L.240, E.244, R.245, A.246, F.389, Y.391, K.395 Ligands: MPD.13 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.221, A:A.224, A:L.240, A:F.389 Hydrogen bonds: A:D.225, A:R.245, A:Y.391, A:K.395 MPD.7: 4 residues within 4Å: Chain A: G.117, W.171, D.429, R.430 5 PLIP interactions: 5 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 MPD.8: 6 residues within 4Å: Chain A: E.104, L.105, A.106, S.136, F.228, S.311 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.106 Hydrogen bonds: A:E.104, A:S.311 MPD.9: 4 residues within 4Å: Chain A: L.316, W.394, P.411, R.413 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.316, A:P.411 Hydrogen bonds: A:W.394, A:R.413 Water bridges: A:R.413 MPD.10: 5 residues within 4Å: Chain A: P.168, M.169, M.272, M.332 Ligands: MPD.14 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.168 Water bridges: A:M.169 MPD.11: 4 residues within 4Å: Chain A: P.5, E.6, N.183, G.184 4 PLIP interactions: 4 interactions with chain A Water bridges: A:E.6, A:A.29, A:A.29, A:G.184 MPD.12: 4 residues within 4Å: Chain A: P.121, P.165, H.166, W.171 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:P.121, A:P.121, A:P.165, A:H.166 Water bridges: A:P.163, A:A.164, A:H.166, A:H.166, A:W.171 MPD.13: 6 residues within 4Å: Chain A: L.233, V.235, E.237, L.238, P.390 Ligands: MPD.6 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.233, A:L.238, A:P.390 Water bridges: A:E.237 MPD.14: 6 residues within 4Å: Chain A: P.168, W.171, M.332, A.333, R.430 Ligands: MPD.10 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.171 MPD.15: 3 residues within 4Å: Chain A: K.81, K.415, G.416 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.415 Water bridges: A:G.416 MPD.16: 4 residues within 4Å: Chain A: P.218, E.234, S.236 Ligands: MPD.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.218 Hydrogen bonds: A:E.234 MPD.17: 3 residues within 4Å: Chain A: N.339, G.340, Q.341 No protein-ligand interaction detected (PLIP) MPD.18: 5 residues within 4Å: Chain A: K.8, L.19, K.20, L.21, G.41 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.19, A:L.21 Hydrogen bonds: A:K.8, A:K.20

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Diaz-Vilchis, A. et al., Preserving metalic sites affected by radiation damage: the CuT2 case in Thermus thermophilus multicopper oxidase. To be Published

Release Date

2017-06-07

Peptides

Laccase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Laccase

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