SMTL ID : 1v0f.1 (1 other biounit)

Endosialidase of Bacteriophage K1F in complex with oligomeric alpha-2,8-sialic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-trimer

Ligands

1 x SIA- SIA: N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid(Non-covalent)

SIA-SIA.1: 12 residues within 4Å: Chain B: T.484, Y.485, S.489 Chain C: F.215, S.216, N.217, S.218, V.220, G.222, V.223, S.224, G.225 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:N.214, C:F.215, C:S.216, C:N.217, C:G.225 Water bridges: C:S.218 Hydrophobic interactions: B:T.484, B:Y.485

3 x SLB: N-acetyl-beta-neuraminic acid(Non-covalent)

SLB.2: 9 residues within 4Å: Chain A: R.593, I.595, T.602, S.603, S.604, Q.609, N.626 Chain B: Y.577 Chain C: Q.633 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:R.593, A:T.602, A:S.604, A:S.604, A:S.604, A:S.604, A:Q.609, A:Q.609, C:Q.633 SLB.4: 6 residues within 4Å: Chain B: R.593, I.595, T.602, S.604, Q.609 Chain C: Y.577 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.593, B:T.602, B:S.604, B:S.604, B:S.604, B:S.604, B:Q.609, B:Q.609 Water bridges: A:Q.633, A:Q.633 SLB.6: 8 residues within 4Å: Chain A: Y.577 Chain C: R.593, I.595, T.602, S.603, S.604, Q.609, N.626 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:R.593, C:T.602, C:S.604, C:S.604, C:S.604, C:S.604, C:Q.609 Water bridges: B:Q.633, B:Q.633

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 6 residues within 4Å: Chain A: E.574, G.575 Chain B: A.561 Chain C: S.583, P.585, T.586 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:G.575, C:S.583, C:T.586 Water bridges: A:E.574, A:E.574, A:E.576, C:D.587 PO4.5: 5 residues within 4Å: Chain A: P.585, T.586 Chain B: E.574, G.575 Chain C: A.561 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: B:G.575, B:G.575, A:T.586 Water bridges: C:A.561, C:A.561 PO4.7: 5 residues within 4Å: Chain A: A.561 Chain B: P.585, T.586 Chain C: E.574, G.575 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:E.574, C:G.575, B:T.586, B:T.586

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stummeyer, K. et al., Crystal Structure of the Polysialic Acid-Degrading Endosialidase of Bacteriophage K1F. Nat.Struct.Mol.Biol. (2005)

Release Date

2004-12-13

Peptides

ENDO-ALPHA-SIALIDASE: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

ENDO-ALPHA-SIALIDASE

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