SMTL ID : 2j3u.1 (1 other biounit)

L-ficolin complexed to galactose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 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: 3 residues within 4Å: Chain B: N.145 Ligands: ACT.3, MAN.8 No protein-ligand interaction detected (PLIP)

3 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.154, D.156, N.158, G.160 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.154, A:D.156, A:N.158 CA.7: 4 residues within 4Å: Chain B: D.154, D.156, N.158, G.160 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.156, B:N.158, B:G.160, H2O.4, H2O.4 CA.13: 4 residues within 4Å: Chain C: D.154, D.156, N.158, G.160 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.154, C:D.154, C:D.156, C:N.158, C:G.160

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

ACT.3: 2 residues within 4Å: Ligands: NAG-NAG.1, NAG-NAG.1 No protein-ligand interaction detected (PLIP) ACT.5: 5 residues within 4Å: Chain B: F.166, N.174, C.175, H.176, Y.204 2 PLIP interactions: 2 interactions with chain B Water bridges: B:C.175 Salt bridges: B:H.176 ACT.12: 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

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.4: 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:R.62, B:D.63 Salt bridges: B:D.63, B:K.151 EPE.10: 4 residues within 4Å: Chain C: R.62, D.63, T.66, K.151 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.63 Salt bridges: C:R.62, C:D.63, C:K.151

2 x GLA: alpha-D-galactopyranose(Non-covalent)

GLA.6: 3 residues within 4Å: Chain B: W.64, D.152, Q.153 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.120, B:E.120, B:D.152, B:D.152 Water bridges: B:W.64, B:A.65 GLA.11: 10 residues within 4Å: Chain B: V.58, G.72, S.73 Chain C: S.21, D.39, D.41, T.42, R.52, E.212, K.214 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:S.21, C:D.39, C:D.41, C:D.41, C:D.41, C:T.42, C:R.52, C:E.212, C:K.214, B:S.73

1 x MAN: alpha-D-mannopyranose(Non-functional Binders)

MAN.8: 1 residues within 4Å: Ligands: NAG-NAG.1 No protein-ligand interaction detected (PLIP)

2 x P4C: O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL(Non-covalent)

P4C.9: 11 residues within 4Å: Chain A: D.55, R.186 Chain B: V.54, D.55, V.101, D.102, F.103, D.105, Y.107, K.209, V.210 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.55, B:K.209, A:R.186 Water bridges: B:R.52 P4C.15: 9 residues within 4Å: Chain B: D.55, G.56, S.57, R.186 Chain C: E.104, D.105, N.106, Y.107, K.209 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.209

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

NAG.14: 1 residues within 4Å: Chain C: N.145 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.145

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Garlatti, V. et al., Structural Insights Into the Innate Immune Recognition Specificities of L- and H-Ficolins. Embo J. (2007)

Release Date

2007-01-23

Peptides

FICOLIN-2: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

FICOLIN-2

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