SMTL ID : 4r9j.1 (3 other biounits)

L-ficolin complexed to glucosamine-6-sulfate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-trimer

Ligands

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

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

4 x CA: CALCIUM ION(Non-functional Binders)(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.153, D.155, N.157, G.159 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.153, A:D.153, A:D.155, A:G.159, H2O.1 CA.7: 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.153, B:D.155, B:G.159, H2O.4 CA.10: 1 residues within 4Å: Chain B: D.151 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.151, H2O.5, H2O.5, H2O.5 CA.14: 4 residues within 4Å: Chain C: D.153, D.155, N.157, G.159 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.153, C:D.153, C:G.159, H2O.9, H2O.9

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

ACT.3: 6 residues within 4Å: Chain A: F.165, N.173, C.174, H.175, A.192, Y.203 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.165, A:A.192, A:Y.203 Hydrogen bonds: A:C.174, A:H.175 ACT.4: 4 residues within 4Å: Chain A: R.73 Chain B: G.21, W.22 Ligands: ACT.13 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Salt bridges: A:R.73 Hydrogen bonds: B:W.22, B:W.22 ACT.5: 6 residues within 4Å: Chain A: D.137, S.138, L.139, T.140, F.141, V.176 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.141 Hydrogen bonds: A:L.139, A:T.140, A:F.141 ACT.8: 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, B:H.175 ACT.9: 3 residues within 4Å: Chain B: E.132, G.133, S.134 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.132, B:G.133 ACT.13: 5 residues within 4Å: Chain B: R.73, L.74 Chain C: G.21, W.22 Ligands: ACT.4 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:W.22 ACT.15: 7 residues within 4Å: Chain C: F.165, N.173, C.174, H.175, F.191, A.192, Y.203 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.165, C:F.191, C:A.192, C:Y.203 Hydrogen bonds: C:C.174, C:H.175, C:H.175

1 x SO4: SULFATE ION

SO4.6: 4 residues within 4Å: Chain A: R.61, D.62, T.65, K.150 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.62, A:T.65 Water bridges: A:R.61, A:R.61 Salt bridges: A:R.61, A:K.150

3 x 3LJ: 2-amino-2-deoxy-6-O-sulfo-alpha-D-glucopyranose(Non-covalent)

3LJ.11: 4 residues within 4Å: Chain B: R.61, D.62, T.65, K.150 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:D.62, B:T.65, B:T.65 Water bridges: B:R.61, B:R.61, B:Q.68, B:Q.68, B:K.150, B:K.150, B:K.150, B:K.150, B:K.150 Salt bridges: B:R.61, B:K.150 3LJ.16: 5 residues within 4Å: Chain A: G.43 Chain C: R.61, D.62, T.65, K.150 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:D.62, C:T.65, C:T.65 Water bridges: C:R.61, C:R.61, A:G.43 Salt bridges: C:R.61, C:K.150 3LJ.17: 4 residues within 4Å: Chain C: R.112, S.113, G.128, A.129 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.129

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

NAG.12: 1 residues within 4Å: Chain B: N.144 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.144

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
G

B
A

C
B

Ficolin-2

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