SMTL ID : 4fj6.1 (1 other biounit)

Crystal structure of a glycoside hydrolase family 33, candidate sialidase (BDI_2946) from Parabacteroides distasonis ATCC 8503 at 1.90 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: S.80, G.485, W.486, E.504, S.505, S.506, A.508, H.509 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.80, A:S.80, A:W.486 GOL.2: 5 residues within 4Å: Chain A: E.257, R.329, I.331, I.432, K.433 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.433 Water bridges: A:T.332, A:T.332 GOL.3: 7 residues within 4Å: Chain A: D.17, R.87, I.168, G.169, V.170, Q.172, W.226 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.87, A:R.87, A:G.169 Water bridges: A:W.226, A:W.226 GOL.4: 5 residues within 4Å: Chain A: R.182, R.201, S.205, V.206, W.486 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.182, A:R.201, A:S.205 Water bridges: A:S.204, A:S.205 GOL.12: 5 residues within 4Å: Chain A: E.91, S.92 Chain B: K.211, K.236, H.243 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.211, B:H.243, A:E.91 Water bridges: B:K.211, B:K.236, B:K.236 GOL.13: 5 residues within 4Å: Chain B: E.257, R.329, I.331, I.432, K.433 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.433 Water bridges: B:E.257, B:E.257, B:L.431 GOL.14: 6 residues within 4Å: Chain B: D.17, R.87, I.168, G.169, V.170, Q.172 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.17, B:R.87, B:R.87, B:G.169 Water bridges: B:R.171, B:W.226, B:W.226

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

PO4.5: 4 residues within 4Å: Chain A: K.211, K.236, Q.237, H.243 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.237 Water bridges: A:K.211, A:H.243, B:E.91, B:E.91 Salt bridges: A:K.211, A:K.236, A:H.243 PO4.6: 5 residues within 4Å: Chain A: R.8, E.70, H.71, F.72, S.73 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.70, A:F.72, A:S.73 Water bridges: A:R.8, A:R.67, A:H.71 Salt bridges: A:R.8, A:H.71 PO4.7: 5 residues within 4Å: Chain A: R.182, D.207, R.393, R.457, Y.488 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.207, A:Y.488 Water bridges: A:R.182, A:R.182, A:R.182 Salt bridges: A:R.182, A:R.393, A:R.457 PO4.8: 2 residues within 4Å: Chain A: H.366, H.368 7 PLIP interactions: 7 interactions with chain A Water bridges: A:Y.357, A:L.367, A:L.367, A:L.367, A:H.368 Salt bridges: A:H.366, A:H.368 PO4.9: 4 residues within 4Å: Chain A: R.218, T.220, E.227, K.303 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.218, A:K.303, A:K.303 Salt bridges: A:R.218, A:K.303 PO4.15: 5 residues within 4Å: Chain B: R.182, D.207, R.393, R.457, Y.488 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:D.207, B:D.207, B:Y.488 Water bridges: B:R.182, B:R.182, B:R.393, B:Y.488, B:Y.488 Salt bridges: B:R.182, B:R.393, B:R.457 PO4.16: 4 residues within 4Å: Chain B: R.8, H.71, F.72, S.73 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:F.72, B:S.73 Water bridges: B:R.8, B:R.8, B:R.8, B:R.8, B:R.67, B:R.67 Salt bridges: B:R.8, B:H.71 PO4.17: 4 residues within 4Å: Chain B: R.218, T.220, E.227, K.303 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.218, B:D.301 Salt bridges: B:R.218, B:K.303

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

CL.10: 2 residues within 4Å: Chain B: Q.31, K.32 Ligand excluded by PLIP CL.11: 1 residues within 4Å: Chain B: E.91 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of a glycoside hydrolase family 33, candidate sialidase (BDI_2946) from Parabacteroides distasonis ATCC 8503 at 1.90 A resolution. To be published

Release Date

2012-07-25

Peptides

glycoside hydrolase family 33, candidate sialidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

glycoside hydrolase family 33, candidate sialidase

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