SMTL ID : 4nyt.1

L-Ficolin Complexed to Phosphocholine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-trimer

Ligands

1 x NAG- NAG- MAN- FUC: alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose(Non-functional Binders)

NAG-NAG-MAN-FUC.1: 2 residues within 4Å: Chain A: N.144, L.156 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.146

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

ACT.2: 7 residues within 4Å: Chain A: F.165, N.173, C.174, H.175, F.191, A.192, Y.203 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.165, A:F.191, A:A.192, A:Y.203 Hydrogen bonds: A:C.174, A:H.175 ACT.5: 7 residues within 4Å: Chain B: F.165, N.173, C.174, H.175, F.191, A.192, Y.203 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.165, B:F.191, B:A.192, B:Y.203 Hydrogen bonds: B:C.174, B:H.175 Salt bridges: B:H.175

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: D.153, D.155, N.157, G.159 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.155, A:N.157, A:G.159, H2O.1, H2O.1 CA.8: 4 residues within 4Å: Chain B: D.153, D.155, N.157, G.159 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.153, B:D.155, B:N.157, B:G.159, H2O.3 CA.9: 1 residues within 4Å: Chain B: D.151 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.151, H2O.3 CA.10: 4 residues within 4Å: Chain C: D.153, D.155, N.157, G.159 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.153, C:D.155, C:N.157, C:G.159

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

PO4.4: 4 residues within 4Å: Chain A: R.61, D.62, T.65, K.150 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.62, A:D.62, A:D.62 Salt bridges: A:R.61, A:K.150

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.6: 1 residues within 4Å: Chain B: N.144 No protein-ligand interaction detected (PLIP)

1 x PC: PHOSPHOCHOLINE(Non-covalent)

PC.7: 4 residues within 4Å: Chain B: R.61, D.62, T.65, K.150 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.62 Salt bridges: B:R.61, B:K.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vassal-Stermann, E. et al., Human L-ficolin recognizes phosphocholine moieties of pneumococcal teichoic Acid. J.Immunol. (2014)

Release Date

2014-10-29

Peptides

Ficolin-2: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

C
B

Ficolin-2