SMTL ID : 4gkx.1 (5 other biounits)

Crystal structure of a carbohydrate-binding domain

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

monomer

Ligands

1 x MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose(Non-covalent)

MAN-MAN.1: 8 residues within 4Å: Chain A: A.111, D.112, F.145, N.147, H.169, G.242, G.243, L.244 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.112, A:D.112, A:N.147, A:G.242, A:G.243, A:L.244 Water bridges: A:D.112, A:H.169

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.143, F.145, N.147, D.172 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.143, A:D.143, A:F.145, A:D.172, H2O.2 CA.3: 5 residues within 4Å: Chain A: D.146, D.148, N.152, N.153, D.172 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.146, A:D.148, A:D.172, H2O.2

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 1 residues within 4Å: Chain A: R.36 No protein-ligand interaction detected (PLIP) GOL.5: 3 residues within 4Å: Chain A: F.220, A.222, K.223 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.223 GOL.6: 4 residues within 4Å: Chain A: N.121, L.134, W.135, N.136 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.121, A:N.136 GOL.7: 3 residues within 4Å: Chain A: K.40, F.57, T.88 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.40 Water bridges: A:T.88 GOL.8: 1 residues within 4Å: Chain A: S.79 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.63, A:Q.80

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Zheng, C. et al., Structural Characterization of Carbohydrate Binding by LMAN1 Protein Provides New Insight into the Endoplasmic Reticulum Export of Factors V (FV) and VIII (FVIII). J.Biol.Chem. (2013)

Release Date

2013-06-05

Peptides

Protein ERGIC-53: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Protein ERGIC-53

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