SMTL ID : 6zqr.2 (1 other biounit)

Crystal structure of tetrameric fibrinogen-like recognition domain of FIBCD1 with GlcNAc ligand bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

homo-tetramer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: D.158, D.160, S.162, N.164 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.158, A:D.158, A:D.160, A:N.164, H2O.1 CA.6: 4 residues within 4Å: Chain B: D.158, D.160, S.162, N.164 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.158, B:D.158, B:D.160, B:N.164, H2O.6 CA.11: 4 residues within 4Å: Chain C: D.158, D.160, S.162, N.164 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.158, C:D.158, C:D.160, C:N.164, H2O.11 CA.16: 4 residues within 4Å: Chain D: D.158, D.160, S.162, N.164 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.158, D:D.158, D:D.160, D:N.164, H2O.16

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

SO4.2: 4 residues within 4Å: Chain A: R.62, G.63, A.66, K.155 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain A Water bridges: C:E.126, A:K.155 Hydrogen bonds: A:G.63 Salt bridges: A:R.62, A:K.155 SO4.3: 2 residues within 4Å: Chain A: H.161, R.177 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.161, A:R.177 SO4.7: 4 residues within 4Å: Chain B: R.62, G.63, A.66, K.155 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:G.63 Water bridges: B:K.155, D:E.126 Salt bridges: B:R.62, B:K.155 SO4.8: 2 residues within 4Å: Chain B: H.161, R.177 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.161, B:R.177 SO4.12: 4 residues within 4Å: Chain C: R.62, G.63, A.66, K.155 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain C Water bridges: B:E.126, C:K.155 Hydrogen bonds: C:G.63 Salt bridges: C:R.62, C:K.155 SO4.13: 2 residues within 4Å: Chain C: H.161, R.177 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:H.161, C:R.177 SO4.17: 4 residues within 4Å: Chain D: R.62, G.63, A.66, K.155 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:G.63 Water bridges: D:K.155, A:E.126 Salt bridges: D:R.62, D:K.155 SO4.18: 2 residues within 4Å: Chain D: H.161, R.177 2 PLIP interactions: 2 interactions with chain D Salt bridges: D:H.161, D:R.177

8 x ACY: ACETIC ACID(Non-functional Binders)

ACY.4: 4 residues within 4Å: Chain A: D.20, Y.37, D.39, E.216 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.37 Salt bridges: A:R.52, A:K.218 ACY.5: 5 residues within 4Å: Chain A: Y.170, N.178, C.179, H.180, W.208 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.208 Hydrogen bonds: A:C.179, A:H.180 Salt bridges: A:H.180 ACY.9: 4 residues within 4Å: Chain B: D.20, Y.37, D.39, E.216 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.37 Salt bridges: B:R.52, B:K.218 ACY.10: 5 residues within 4Å: Chain B: Y.170, N.178, C.179, H.180, W.208 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.208 Hydrogen bonds: B:C.179, B:H.180 Salt bridges: B:H.180 ACY.14: 4 residues within 4Å: Chain C: D.20, Y.37, D.39, E.216 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:Y.37 Salt bridges: C:R.52, C:K.218 ACY.15: 5 residues within 4Å: Chain C: Y.170, N.178, C.179, H.180, W.208 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:W.208 Hydrogen bonds: C:C.179, C:H.180 Salt bridges: C:H.180 ACY.19: 4 residues within 4Å: Chain D: D.20, Y.37, D.39, E.216 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:Y.37 Salt bridges: D:R.52, D:K.218 ACY.20: 5 residues within 4Å: Chain D: Y.170, N.178, C.179, H.180, W.208 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:W.208 Hydrogen bonds: D:C.179, D:H.180 Salt bridges: D:H.180

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Williams, H.M. et al., Crystal structures of human immune protein FIBCD1 suggest an extended binding site compatible with recognition of pathogen associated carbohydrate motifs. J.Biol.Chem. (2023)

Release Date

2021-07-21

Peptides

Fibrinogen C domain-containing protein 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

C
B

D
B

Fibrinogen C domain-containing protein 1

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