SMTL ID : 1fih.1

N-ACETYLGALACTOSAMINE BINDING MUTANT OF MANNOSE-BINDING PROTEIN A (QPDWG-HDRPY), COMPLEX WITH N-ACETYLGALACTOSAMINE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-trimer

Ligands

4 x NGA: 2-acetamido-2-deoxy-beta-D-galactopyranose(Non-covalent)

NGA.1: 9 residues within 4Å: Chain A: Q.113, D.115, W.117, E.126, H.130, N.138, D.139, Y.146 Ligands: CA.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.113, A:D.115, A:N.138 Water bridges: A:D.140, A:Y.146 NGA.6: 9 residues within 4Å: Chain B: Q.113, D.115, W.117, E.126, H.130, N.138, D.139, D.140 Ligands: CA.8 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.113, B:E.126, B:N.138, B:D.140, B:D.140 NGA.11: 8 residues within 4Å: Chain C: Q.113, D.115, W.117, E.126, H.130, N.138, D.139 Ligands: CA.14 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Q.113, C:D.115, C:N.138 Water bridges: C:D.140, C:Y.146 Salt bridges: C:K.110 NGA.12: 6 residues within 4Å: Chain A: E.58 Chain C: K.25, A.28, F.29, K.33, S.35 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:A.28, C:S.35, A:E.58, A:E.58 Water bridges: C:G.36 Salt bridges: C:K.33

9 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: D.89, E.93, D.116, E.126, D.127 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.89, A:E.93, A:D.116, A:D.127, H2O.3 CA.3: 6 residues within 4Å: Chain A: Q.113, D.115, E.126, N.138, D.139 Ligands: NGA.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.115, A:E.126, A:D.139, A:D.139 CA.4: 1 residues within 4Å: Chain A: E.12 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.12, H2O.3 CA.7: 6 residues within 4Å: Chain B: D.89, E.93, D.116, E.126, D.127 Ligands: CA.9 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.89, B:D.89, B:E.93, B:D.116, B:D.127 CA.8: 6 residues within 4Å: Chain B: Q.113, D.115, E.126, N.138, D.139 Ligands: NGA.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.115, B:E.126, B:D.139, B:D.139 CA.9: 3 residues within 4Å: Chain B: E.93, D.127 Ligands: CA.7 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.93, B:D.127, B:D.127, H2O.3, H2O.5 CA.13: 5 residues within 4Å: Chain C: D.89, E.93, D.116, E.126, D.127 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.89, C:E.93, C:D.116, C:D.127, H2O.7 CA.14: 6 residues within 4Å: Chain C: Q.113, D.115, E.126, N.138, D.139 Ligands: NGA.11 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.115, C:E.126, C:D.139, C:D.139 CA.15: 1 residues within 4Å: Chain C: E.12 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.12, H2O.3, H2O.7, H2O.7

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 5 residues within 4Å: Chain A: G.125, E.126, D.127, S.141, C.142 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain B: G.125, D.127, S.141, C.142 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain C: G.125, E.126, D.127, S.141, C.142 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Feinberg, H. et al., Mechanism of pH-dependent N-acetylgalactosamine binding by a functional mimic of the hepatocyte asialoglycoprotein receptor. J.Biol.Chem. (2000)

Release Date

2000-08-23

Peptides

MANNOSE-BINDING PROTEIN A: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

MANNOSE-BINDING PROTEIN A

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