SMTL ID : 3f53.1

Crystal structure of Toxoplasma gondii micronemal protein 1 bound to 2F-3'SiaLacNAc

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x 2FG- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-2-deoxy-2-fluoro-beta-D-galactopyranose(Non-covalent)

2FG-SIA.1: 5 residues within 4Å: Chain A: K.200, R.201, H.202, Y.203, T.204 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.202, A:H.202, A:T.204 Salt bridges: A:H.202

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

CL.2: 6 residues within 4Å: Chain A: S.17, D.89, D.90, C.187, P.188 Ligands: GOL.11 Ligand excluded by PLIP

8 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 5 residues within 4Å: Chain A: N.86, T.94, P.96, K.166, A.167 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.94 Salt bridges: A:K.166 ACT.4: 3 residues within 4Å: Chain A: M.24, R.28, L.118 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.28 ACT.5: 3 residues within 4Å: Chain A: P.47, S.48, S.49 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.48, A:S.49, A:S.49 ACT.6: 5 residues within 4Å: Chain A: Q.62, H.108, A.109, T.110 Ligands: ACT.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.62, A:T.110, A:T.110 Salt bridges: A:H.108 ACT.7: 6 residues within 4Å: Chain A: P.96, C.97, P.98, L.170, Y.171, S.172 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.170 Hydrogen bonds: A:P.96, A:Y.171, A:S.172 ACT.8: 6 residues within 4Å: Chain A: K.43, I.59, S.106, N.107, H.108 Ligands: ACT.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.108 Salt bridges: A:K.43, A:H.108 ACT.9: 7 residues within 4Å: Chain A: W.161, E.176, C.177, A.178, G.182, T.183, T.184 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.178 Hydrogen bonds: A:C.177 ACT.10: 5 residues within 4Å: Chain A: R.19, Q.22, Q.23, D.26, Y.171 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Q.22, A:Q.23 Water bridges: A:R.54, A:R.54 Salt bridges: A:R.19

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 10 residues within 4Å: Chain A: S.17, D.90, C.91, F.126, C.127, S.128, W.185, C.187, D.230 Ligands: CL.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.128 Water bridges: A:G.18, A:C.91, A:C.91 GOL.12: 3 residues within 4Å: Chain A: Y.20, D.230, E.231 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.230 Water bridges: A:D.230 GOL.13: 2 residues within 4Å: Chain A: E.31, E.35 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.31, A:E.35 GOL.14: 9 residues within 4Å: Chain A: G.92, H.93, T.94, N.139, G.144, T.145, I.146, K.166 Ligands: GOL.15 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.92, A:H.93, A:T.94, A:T.145 GOL.15: 6 residues within 4Å: Chain A: C.91, G.92, H.93, V.119, E.120 Ligands: GOL.14 3 PLIP interactions: 3 interactions with chain A Water bridges: A:C.91, A:E.120, A:E.120

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Garnett, J.A. et al., Detailed insights from microarray and crystallographic studies into carbohydrate recognition by microneme protein 1 (MIC1) of Toxoplasma gondii. Protein Sci. (2009)

Release Date

2009-07-28

Peptides

Micronemal protein 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Micronemal protein 1

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