SMTL ID : 4m7f.1 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 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.5: 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.7 CA.9: 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.13 CA.13: 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.19

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

NAG.2: 1 residues within 4Å: Chain A: N.105 No protein-ligand interaction detected (PLIP) NAG.6: 1 residues within 4Å: Chain B: N.105 No protein-ligand interaction detected (PLIP) NAG.10: 1 residues within 4Å: Chain C: N.105 No protein-ligand interaction detected (PLIP) NAG.14: 1 residues within 4Å: Chain D: N.105 No protein-ligand interaction detected (PLIP)

4 x BM3: 2-acetamido-2-deoxy-alpha-D-mannopyranose(Non-covalent)

BM3.3: 7 residues within 4Å: Chain A: Y.170, N.178, C.179, H.180, Y.196, A.197, W.208 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.196, A:A.197, A:W.208 Hydrogen bonds: A:C.179, A:H.180, A:Y.196 Water bridges: A:Y.170 BM3.7: 7 residues within 4Å: Chain B: Y.170, N.178, C.179, H.180, Y.196, A.197, W.208 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.196, B:A.197, B:W.208 Hydrogen bonds: B:C.179, B:H.180, B:Y.196 Water bridges: B:Y.170 BM3.11: 7 residues within 4Å: Chain C: Y.170, N.178, C.179, H.180, Y.196, A.197, W.208 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:Y.196, C:A.197, C:W.208 Hydrogen bonds: C:C.179, C:H.180, C:Y.196 Water bridges: C:Y.170 BM3.15: 7 residues within 4Å: Chain D: Y.170, N.178, C.179, H.180, Y.196, A.197, W.208 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:Y.196, D:A.197, D:W.208 Hydrogen bonds: D:C.179, D:H.180, D:Y.196 Water bridges: D:Y.170

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

SO4.4: 5 residues within 4Å: Chain A: F.61, R.62, G.63, A.66, K.155 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.63 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 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.63 Salt bridges: B:R.62, B:K.155 SO4.12: 5 residues within 4Å: Chain C: F.61, R.62, G.63, A.66, K.155 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.63 Salt bridges: C:R.62, C:K.155 SO4.16: 5 residues within 4Å: Chain D: F.61, R.62, G.63, A.66, K.155 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.63 Salt bridges: D:R.62, D:K.155

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Shrive, A.K. et al., Crystal Structure of the Tetrameric Fibrinogen-like Recognition Domain of Fibrinogen C Domain Containing 1 (FIBCD1) Protein. J.Biol.Chem. (2014)

Release Date

2013-12-11

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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