SMTL ID : 6zqy.1 (1 other biounit)

Crystal structure of tetrameric fibrinogen-like recognition domain of FIBCD1 with Neu5Ac ligand bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-tetramer

Ligands

4 x NAG- FUC- NAG: alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-FUC-NAG.1: 1 residues within 4Å: Chain A: N.105 No protein-ligand interaction detected (PLIP) NAG-FUC-NAG.6: 1 residues within 4Å: Chain B: N.105 No protein-ligand interaction detected (PLIP) NAG-FUC-NAG.11: 1 residues within 4Å: Chain C: N.105 No protein-ligand interaction detected (PLIP) NAG-FUC-NAG.16: 1 residues within 4Å: Chain D: N.105 No protein-ligand interaction detected (PLIP)

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 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.2 CA.7: 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.9 CA.12: 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.15 CA.17: 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.22

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

SO4.3: 5 residues within 4Å: Chain A: F.61, R.62, G.63, A.66, K.155 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.63 Water bridges: A:N.59, A:A.66 Salt bridges: A:R.62, A:K.155 SO4.8: 5 residues within 4Å: Chain B: F.61, R.62, G.63, A.66, K.155 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.63 Water bridges: B:N.59, B:A.66 Salt bridges: B:R.62, B:K.155 SO4.13: 5 residues within 4Å: Chain C: F.61, R.62, G.63, A.66, K.155 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.63 Water bridges: C:N.59, C:A.66 Salt bridges: C:R.62, C:K.155 SO4.18: 5 residues within 4Å: Chain D: F.61, R.62, G.63, A.66, K.155 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:G.63 Water bridges: D:N.59, D:A.66 Salt bridges: D:R.62, D:K.155

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

ACY.4: 2 residues within 4Å: Chain A: A.168, R.171 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.171 ACY.9: 2 residues within 4Å: Chain B: A.168, R.171 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.171 ACY.14: 2 residues within 4Å: Chain C: A.168, R.171 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.171 ACY.19: 2 residues within 4Å: Chain D: A.168, R.171 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.171

4 x SLB: N-acetyl-beta-neuraminic acid(Non-covalent)

SLB.5: 7 residues within 4Å: Chain A: Y.170, N.178, C.179, H.180, Y.196, A.197, W.208 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.170, A:Y.196, A:A.197, A:W.208 Hydrogen bonds: A:Y.170, A:N.178, A:C.179, A:H.180, A:Y.196, A:Y.196, A:Y.196 Water bridges: A:Y.170, A:N.178 SLB.10: 7 residues within 4Å: Chain B: Y.170, N.178, C.179, H.180, Y.196, A.197, W.208 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Y.170, B:Y.196, B:A.197, B:W.208 Hydrogen bonds: B:Y.170, B:N.178, B:C.179, B:H.180, B:Y.196, B:Y.196, B:Y.196 Water bridges: B:Y.170, B:N.178 SLB.15: 7 residues within 4Å: Chain C: Y.170, N.178, C.179, H.180, Y.196, A.197, W.208 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:Y.170, C:Y.196, C:A.197, C:W.208 Hydrogen bonds: C:Y.170, C:N.178, C:C.179, C:H.180, C:Y.196, C:Y.196, C:Y.196 Water bridges: C:Y.170, C:N.178 SLB.20: 7 residues within 4Å: Chain D: Y.170, N.178, C.179, H.180, Y.196, A.197, W.208 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:Y.170, D:Y.196, D:A.197, D:W.208 Hydrogen bonds: D:Y.170, D:N.178, D:C.179, D:H.180, D:Y.196, D:Y.196, D:Y.196 Water bridges: D:Y.170, D:N.178

Links

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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
A

B
A

C
A

D
A

Fibrinogen C domain-containing protein 1

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