SMTL ID : 1jif.1

Crystal structure of bleomycin-binding protein from bleomycin-producing Streptomyces verticillus complexed with copper(II)-bleomycin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x CU: COPPER (II) ION(Non-functional Binders)

CU.1: 2 residues within 4Å: Ligands: CL.2, BLM.6 No protein-ligand interaction detected (PLIP) CU.3: 2 residues within 4Å: Ligands: CL.4, BLM.5 No protein-ligand interaction detected (PLIP)

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 2 residues within 4Å: Ligands: CU.1, BLM.6 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Ligands: CU.3, BLM.5 Ligand excluded by PLIP

2 x BLM: BLEOMYCIN A2(Non-covalent)

BLM.5: 23 residues within 4Å: Chain A: D.32, F.33, F.38, H.49, S.51, R.52 Chain B: A.59, D.60, N.61, T.62, W.65, Y.86, A.87, P.101, A.102, A.107, R.109, G.113, N.114, C.115, H.117 Ligands: CU.3, CL.4 17 PLIP interactions: 12 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:W.65, B:A.107, B:R.109, A:F.38, A:F.38 Hydrogen bonds: B:D.60, B:T.62, B:Y.86, B:R.109, B:R.109, B:G.113, B:C.115, A:S.51, A:R.52 Water bridges: B:N.61, B:H.117 pi-Stacking: A:F.33 BLM.6: 21 residues within 4Å: Chain A: A.59, D.60, N.61, T.62, W.65, Y.86, A.87, P.101, A.107, R.109, G.113, N.114, C.115, H.117 Chain B: F.33, F.38, H.49, S.51, R.52 Ligands: CU.1, CL.2 18 PLIP interactions: 14 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:A.107, A:R.109, B:F.38 Hydrogen bonds: A:D.60, A:D.60, A:T.62, A:R.109, A:R.109, A:G.113, A:C.115, B:S.51, B:R.52 Water bridges: A:N.61, A:S.63, A:E.105, A:H.117, A:H.117 pi-Stacking: B:F.33

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sugiyama, M. et al., The 1.6-A crystal structure of the copper(II)-bound bleomycin complexed with the bleomycin-binding protein from bleomycin-producing Streptomyces verticillus. J.Biol.Chem. (2002)

Release Date

2002-02-06

Peptides

bleomycin-binding protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

bleomycin-binding protein

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