SMTL ID : 2z3i.1

Crystal structure of blasticidin S deaminase (BSD) mutant E56Q complexed with substrate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

4 x BLS: BLASTICIDIN S(Non-covalent)

BLS.1: 19 residues within 4Å: Chain A: E.25, D.26, S.28, V.29, N.45, Y.47, C.54, A.55, Q.56, A.76, R.82, S.86, P.87, C.88 Chain B: Y.126, W.128 Chain C: F.49 Chain D: W.128, G.130 15 PLIP interactions: 11 interactions with chain A, 1 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: A:Y.47, C:F.49 Hydrogen bonds: A:E.25, A:S.28, A:S.28, A:A.55, A:Q.56, A:S.86, A:C.88, B:Y.126 Salt bridges: A:E.25, A:D.26, A:R.82 Water bridges: B:E.129 pi-Stacking: B:Y.126 BLS.4: 18 residues within 4Å: Chain A: Y.126, W.128 Chain B: E.25, D.26, S.28, V.29, N.45, Y.47, C.54, A.55, Q.56, A.76, R.82, S.86, P.87, C.88 Chain C: W.128 Chain D: F.49 17 PLIP interactions: 12 interactions with chain B, 4 interactions with chain A, 1 interactions with chain D Hydrogen bonds: B:E.25, B:S.28, B:S.28, B:A.55, B:Q.56, B:S.86, B:C.88, A:Y.126, A:Y.126 Water bridges: B:R.82, B:R.82, A:E.129 Salt bridges: B:E.25, B:D.26, B:R.82 pi-Stacking: A:Y.126 Hydrophobic interactions: D:F.49 BLS.7: 17 residues within 4Å: Chain A: F.49 Chain B: G.130 Chain C: E.25, D.26, S.28, V.29, N.45, Y.47, C.54, A.55, Q.56, R.82, S.86, P.87, C.88 Chain D: Y.126, W.128 19 PLIP interactions: 9 interactions with chain C, 2 interactions with chain B, 5 interactions with chain D, 3 interactions with chain A Hydrogen bonds: C:S.28, C:S.28, C:A.55, C:Q.56, C:S.86, C:C.88, B:G.130, D:Y.126, D:Y.126 Water bridges: C:N.45, B:G.130, D:G.130, D:G.130, A:Y.47 Salt bridges: C:E.25, C:R.82 pi-Stacking: D:Y.126 Hydrophobic interactions: A:F.49, A:F.49 BLS.10: 21 residues within 4Å: Chain A: W.128, E.129 Chain B: F.49 Chain C: Y.126, W.128, E.129 Chain D: E.25, D.26, S.28, V.29, N.45, Y.47, C.54, A.55, Q.56, A.76, R.82, L.85, S.86, P.87, C.88 17 PLIP interactions: 1 interactions with chain A, 11 interactions with chain D, 3 interactions with chain C, 2 interactions with chain B Salt bridges: A:E.129, D:E.25, D:D.26, D:R.82 Hydrophobic interactions: D:Y.47, B:F.49, B:F.49 Hydrogen bonds: D:E.25, D:S.28, D:S.28, D:A.55, D:Q.56, D:S.86, D:C.88, C:Y.126, C:E.129 pi-Stacking: C:Y.126

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 3 residues within 4Å: Chain A: C.54, C.88, C.91 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:C.54, A:C.88, A:C.91, H2O.3, H2O.6 ZN.5: 3 residues within 4Å: Chain B: C.54, C.88, C.91 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:C.54, B:C.88, B:C.91, H2O.8, H2O.11 ZN.8: 3 residues within 4Å: Chain C: C.54, C.88, C.91 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:C.54, C:C.88, C:C.91, H2O.13, H2O.17 ZN.11: 3 residues within 4Å: Chain D: C.54, C.88, C.91 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:C.54, D:C.88, D:C.91, H2O.19, H2O.22

4 x CAC: CACODYLATE ION(Non-covalent)

CAC.3: 6 residues within 4Å: Chain A: S.4, E.6, E.7, T.72, C.73, A.115 No protein-ligand interaction detected (PLIP) CAC.6: 6 residues within 4Å: Chain B: S.4, E.7, T.72, C.73, K.103, A.115 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.72 CAC.9: 7 residues within 4Å: Chain C: E.6, E.7, L.10, C.73, K.103, I.105, A.115 No protein-ligand interaction detected (PLIP) CAC.12: 7 residues within 4Å: Chain D: E.6, E.7, T.72, C.73, K.103, I.105, A.115 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.72

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumasaka, T. et al., Crystal structures of blasticidin S deaminase (BSD): implications for dynamic properties of catalytic zinc. J.Biol.Chem. (2007)

Release Date

2007-10-23

Peptides

Blasticidin-S deaminase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Blasticidin-S deaminase