SMTL ID : 2kmb.1

COMPLEX OF 3'-NEUAC-LEWIS-X WITH A SELECTIN-LIKE MUTANT OF MANNOSE-BINDING PROTEIN A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-trimer

Ligands

2 x MAG- GAL- SIA- FUC: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]methyl 2-acetamido-2-deoxy-beta-D-glucopyranoside

MAG-GAL-SIA-FUC.1: 10 residues within 4Å: Chain A: D.112, E.113, N.115, H.117, E.121, N.133, D.134, I.135, K.139 Ligands: CA.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.113, A:N.115, A:E.121, A:N.133, A:E.121, A:E.121, A:K.139, A:N.115 Hydrophobic interactions: A:D.112 Salt bridges: A:H.117, A:K.139 MAG-GAL-SIA-FUC.2: 9 residues within 4Å: Chain B: D.112, E.113, N.115, H.117, E.121, N.133, D.134, K.139 Ligands: CA.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.113, B:N.115, B:E.121, B:N.133, B:H.117, B:K.139, B:N.115 Water bridges: B:S.119, B:E.121 Hydrophobic interactions: B:D.112 Salt bridges: B:H.117

1 x NAG- GAL- SIA- FUC: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-GAL-SIA-FUC.3: 8 residues within 4Å: Chain C: E.113, N.115, H.117, E.121, N.133, D.134, K.139 Ligands: CA.14 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.113, C:N.115, C:E.121, C:N.133, C:H.117, C:K.139, C:N.115 Water bridges: C:K.139, C:S.119, C:G.120 Salt bridges: C:K.139, C:H.117

10 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.4: 5 residues within 4Å: Chain A: D.89, E.93, D.116, E.121, D.122 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.122, H2O.3 CA.5: 6 residues within 4Å: Chain A: E.113, N.115, E.121, N.133, D.134 Ligands: MAG-GAL-SIA-FUC.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.113, A:E.121, A:D.134, A:D.134 CA.6: 2 residues within 4Å: Chain A: E.93, D.122 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.93, A:D.122, H2O.3, H2O.4, H2O.4 CA.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.9: 6 residues within 4Å: Chain B: D.89, E.93, D.116, E.121, D.122 Ligands: CA.11 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.89, B:D.89, B:E.93, B:D.116, H2O.9 CA.10: 6 residues within 4Å: Chain B: E.113, N.115, E.121, N.133, D.134 Ligands: MAG-GAL-SIA-FUC.2 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.113, B:E.121, B:D.134, B:D.134 CA.11: 4 residues within 4Å: Chain B: E.93, D.116, D.122 Ligands: CA.9 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.93, H2O.8, H2O.8, H2O.8, H2O.8 CA.13: 6 residues within 4Å: Chain C: D.89, E.93, D.116, E.121, D.122 Ligands: CA.15 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.122, H2O.16 CA.14: 6 residues within 4Å: Chain C: E.113, N.115, E.121, N.133, D.134 Ligands: NAG-GAL-SIA-FUC.3 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.113, C:E.121, C:D.134, C:D.134 CA.15: 3 residues within 4Å: Chain C: E.93, D.122 Ligands: CA.13 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.93, C:D.122, C:D.122, H2O.17

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

CL.8: 3 residues within 4Å: Chain A: D.122, S.136, C.137 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain B: G.120, E.121, D.122, S.136, C.137 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain C: E.121, D.122, S.136, C.137 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ng, K.K. et al., Structure of a selectin-like mutant of mannose-binding protein complexed with sialylated and sulfated Lewis(x) oligosaccharides. Biochemistry (1997)

Release Date

1997-02-12

Peptides

MANNOSE-BINDING PROTEIN-A: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

B
2

C
3

MANNOSE-BINDING PROTEIN-A

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