SMTL ID : 4r9t.1 (3 other biounits)

L-ficolin complexed to sulphates

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-trimer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 1 residues within 4Å: Chain A: N.145 No protein-ligand interaction detected (PLIP)

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

ACT.2: 6 residues within 4Å: Chain A: F.166, N.174, C.175, H.176, F.192, Y.204 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.166, A:F.192, A:Y.204 Hydrogen bonds: A:C.175, A:H.176 ACT.8: 7 residues within 4Å: Chain C: F.166, N.174, C.175, H.176, F.192, A.193, Y.204 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.166, C:F.192, C:A.193, C:Y.204 Hydrogen bonds: C:C.175, C:H.176

3 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: D.154, D.156, N.158, G.160 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.156, A:N.158, A:G.160, H2O.1, H2O.1 CA.6: 4 residues within 4Å: Chain B: D.154, D.156, N.158, G.160 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.154, B:D.156, B:N.158, B:G.160, H2O.2 CA.9: 4 residues within 4Å: Chain C: D.154, D.156, N.158, G.160 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.154, C:D.154, C:G.160, H2O.2, H2O.2

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 5 residues within 4Å: Chain A: Y.61, R.62, D.63, T.66, K.151 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.63 Salt bridges: A:R.62, A:K.151 SO4.5: 3 residues within 4Å: Chain A: H.189, G.190, S.191 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.190, A:S.191 SO4.7: 4 residues within 4Å: Chain B: R.62, D.63, T.66, K.151 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.63, B:T.66 Salt bridges: B:R.62, B:K.151 SO4.10: 4 residues within 4Å: Chain C: R.62, D.63, T.66, K.151 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.63 Salt bridges: C:R.62, C:K.151

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Laffly, E. et al., Human ficolin-2 recognition versatility extended: An update on the binding of ficolin-2 to sulfated/phosphated carbohydrates. Febs Lett. (2014)

Release Date

2014-11-05

Peptides

Ficolin-2: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
C

Ficolin-2

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