SMTL ID : 2zhp.1

Crystal structure of bleomycin-binding protein from Streptoalloteichus hindustanus complexed with bleomycin derivative

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x BY6: [(2S,3R,4R,5S,6S)-2-[(3R,4R,5R,6R)-2-[(1R,2S)-2-[[6-amino-2-[(1S)-3-amino-1-[(2,3-diamino-3-oxopropyl)amino]-3-oxopropyl]-5-methylpyrimidine-4-carbonyl]amino]-3-[[(2S,3R,4R)-5-[[(2R,3S)-1-[2-[4-[4-[3-[4-(3-aminopropylamino)butylamino]propylcarbamoyl]-1,3-thiazol-2-yl]-1,3-thiazol-2-yl]ethylamino]-3-hydroxy-1-oxobutan-2-yl]amino]-3-hydroxy-4-methyl-5-oxopentan-2-yl]amino]-1-(3H-imidazol-4-yl)-3-oxopropoxy]-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl]oxy-3,5-dihydroxy-6-(hydroxymethyl)oxan-4-yl] carbamate(Non-covalent)

BY6.1: 25 residues within 4Å: Chain A: P.59, D.60, N.61, T.62, L.63, W.65, F.86, R.87, T.95, W.102, A.107, R.109, G.113, N.114, C.115, H.117 Chain B: F.33, E.35, F.38, F.49, S.51, A.52, V.53 Ligands: CU.2, CL.3 23 PLIP interactions: 18 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:L.63, A:W.65, A:F.86, A:T.95, A:A.107, A:R.109, B:F.38, B:F.38 Hydrogen bonds: A:D.60, A:T.62, A:F.86, A:R.109, A:R.109, A:G.113, A:C.115, B:S.51, B:A.52 Water bridges: A:Q.100, A:H.117, A:H.117 pi-Stacking: A:W.102, A:W.102, B:F.33 BY6.4: 20 residues within 4Å: Chain A: F.33, E.35, F.38, F.49, A.52, V.53 Chain B: P.59, D.60, N.61, T.62, L.63, W.65, T.95, A.107, R.109, G.113, C.115, H.117 Ligands: CU.5, CL.6 13 PLIP interactions: 5 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:F.38, A:F.38, B:W.65, B:T.95, B:A.107, B:R.109 Hydrogen bonds: A:S.51, A:A.52, B:D.60, B:T.62, B:R.109, B:G.113 pi-Stacking: A:F.33

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

CU.2: 2 residues within 4Å: Ligands: BY6.1, CL.3 No protein-ligand interaction detected (PLIP) CU.5: 2 residues within 4Å: Ligands: BY6.4, CL.6 No protein-ligand interaction detected (PLIP)

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

CL.3: 5 residues within 4Å: Chain A: L.63, C.115, H.117 Ligands: BY6.1, CU.2 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain B: L.63, H.117 Ligands: BY6.4, CU.5 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain B: E.21, D.25 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miyazaki, I. et al., Structure-Affinity Relationship Study of Bleomycins and Shble protein Using a Chemical Array. To be Published

Release Date

2009-02-17

Peptides

Bleomycin resistance protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Bleomycin resistance protein