SMTL ID : 2z3h.1

Crystal structure of blasticidin S deaminase (BSD) complexed with deaminohydroxy blasticidin S

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.54, C.88, C.91 Ligands: BLO.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.54, A:C.88, A:C.91 ZN.3: 4 residues within 4Å: Chain B: C.54, C.88, C.91 Ligands: BLO.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.54, B:C.88, B:C.91 ZN.5: 4 residues within 4Å: Chain C: C.54, C.88, C.91 Ligands: BLO.6 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.54, C:C.88, C:C.91 ZN.7: 4 residues within 4Å: Chain D: C.54, C.88, C.91 Ligands: BLO.8 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.54, D:C.88, D:C.91, H2O.25

4 x BLO: 1-(4-{[(3R)-3-AMINO-5-{[(Z)-AMINO(IMINO)METHYL](METHYL)AMINO}PENTANOYL]AMINO}-2,3,4-TRIDEOXY-D-ERYTHRO-HEX-2-ENOPYRANURONOSYL)-4-HYDROXYPYRIMIDIN-2(1H)-ONE(Non-covalent)

BLO.2: 17 residues within 4Å: Chain A: E.25, D.26, S.28, V.29, N.45, Y.47, C.54, A.55, E.56, R.82, P.87, C.88, C.91 Chain B: Y.126, W.128 Chain C: F.49 Ligands: ZN.1 11 PLIP interactions: 1 interactions with chain B, 8 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: B:Y.126, C:F.49, C:F.49 Hydrogen bonds: A:S.28, A:S.28, A:S.28, A:A.55, A:C.88 Water bridges: A:N.45 Salt bridges: A:E.25, A:R.82 BLO.4: 15 residues within 4Å: Chain B: E.25, D.26, S.28, V.29, N.45, Y.47, C.54, A.55, E.56, R.82, P.87, C.88, C.91 Chain D: F.49 Ligands: ZN.3 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:S.28, B:S.28, B:S.28, B:A.55, B:C.88 Water bridges: B:E.25, B:N.45 Salt bridges: B:E.25, B:D.26, B:R.82 Hydrophobic interactions: D:F.49, D:F.49 BLO.6: 15 residues within 4Å: Chain A: F.49 Chain C: E.25, D.26, S.28, V.29, N.45, Y.47, C.54, A.55, E.56, R.82, P.87, C.88, C.91 Ligands: ZN.5 15 PLIP interactions: 13 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:E.25, C:S.28, C:S.28, C:S.28, C:A.55, C:C.88 Water bridges: C:D.26, C:D.26, C:D.26, C:N.45 Salt bridges: C:E.25, C:D.26, C:R.82 Hydrophobic interactions: A:F.49, A:F.49 BLO.8: 15 residues within 4Å: Chain B: F.49 Chain D: E.25, D.26, S.28, V.29, N.45, Y.47, C.54, A.55, E.56, R.82, P.87, C.88, C.91 Ligands: ZN.7 11 PLIP interactions: 9 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:S.28, D:S.28, D:S.28, D:A.55, D:C.88 Water bridges: D:N.45 Salt bridges: D:E.25, D:D.26, D:R.82 Hydrophobic interactions: B:F.49, B:F.49

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

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