SMTL ID : 1npl.1 (1 other biounit)

MANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM DAFFODIL (NARCISSUS PSEUDONARCISSUS) BULBS IN COMPLEX WITH MANNOSE-ALPHA1,3-MANNOSE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

16 x MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose(Non-covalent)

MAN-MAN.1: 10 residues within 4Å: Chain A: Q.89, D.91, N.93, V.95, Y.97 Chain C: N.83, A.100, A.103, N.107, H.109 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:Q.89, A:D.91, A:N.93, A:Y.97, A:Y.97 Water bridges: C:Y.84 MAN-MAN.2: 5 residues within 4Å: Chain A: Q.26, D.28, N.30, Y.34 Chain D: D.37 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Water bridges: A:Q.26, A:D.28, A:Y.34 Hydrogen bonds: D:D.37 MAN-MAN.3: 7 residues within 4Å: Chain A: Q.57, D.59, N.61, Y.65, P.71, A.74 Ligands: PO4.7 No protein-ligand interaction detected (PLIP) MAN-MAN.4: 6 residues within 4Å: Chain A: W.41, A.42, T.43, N.44, W.73 Chain C: W.102 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.44 MAN-MAN.8: 10 residues within 4Å: Chain B: Q.89, D.91, N.93, V.95, Y.97 Chain D: N.83, A.100, A.103, N.107, H.109 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:Q.89, B:D.91, B:N.93, B:Y.97, B:Y.97 Water bridges: D:Y.84 MAN-MAN.9: 5 residues within 4Å: Chain B: Q.26, D.28, N.30, Y.34 Chain C: D.37 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Water bridges: B:Q.26, B:D.28, B:Y.34 Hydrogen bonds: C:D.37 MAN-MAN.10: 7 residues within 4Å: Chain B: Q.57, D.59, N.61, Y.65, P.71, A.74 Ligands: PO4.14 No protein-ligand interaction detected (PLIP) MAN-MAN.11: 6 residues within 4Å: Chain B: W.41, A.42, T.43, N.44, W.73 Chain D: W.102 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.44 MAN-MAN.15: 10 residues within 4Å: Chain A: N.83, A.100, A.103, N.107, H.109 Chain C: Q.89, D.91, N.93, V.95, Y.97 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Q.89, C:D.91, C:N.93, C:Y.97, C:Y.97 Water bridges: A:Y.84 MAN-MAN.16: 5 residues within 4Å: Chain B: D.37 Chain C: Q.26, D.28, N.30, Y.34 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Water bridges: C:Q.26, B:D.37 Hydrogen bonds: B:D.37 MAN-MAN.17: 7 residues within 4Å: Chain C: Q.57, D.59, N.61, Y.65, P.71, A.74 Ligands: PO4.21 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.59 MAN-MAN.18: 6 residues within 4Å: Chain A: W.102 Chain C: W.41, A.42, T.43, N.44, W.73 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.44 MAN-MAN.22: 10 residues within 4Å: Chain B: N.83, A.100, A.103, N.107, H.109 Chain D: Q.89, D.91, N.93, V.95, Y.97 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:Q.89, D:D.91, D:N.93, D:Y.97, D:Y.97 Water bridges: B:Y.84 MAN-MAN.23: 5 residues within 4Å: Chain A: D.37 Chain D: Q.26, D.28, N.30, Y.34 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A Water bridges: D:Q.26, A:D.37 Hydrogen bonds: A:D.37 MAN-MAN.24: 7 residues within 4Å: Chain D: Q.57, D.59, N.61, Y.65, P.71, A.74 Ligands: PO4.28 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.59 MAN-MAN.25: 6 residues within 4Å: Chain B: W.102 Chain D: W.41, A.42, T.43, N.44, W.73 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.44

12 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 7 residues within 4Å: Chain A: D.1, I.3, Y.5 Chain C: N.2, N.18, Q.89, K.90 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:D.1, A:Y.5, C:N.2, C:N.18, C:K.90 PO4.6: 3 residues within 4Å: Chain A: K.38, I.40, R.92 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.92 Salt bridges: A:K.38, A:R.92 PO4.7: 3 residues within 4Å: Chain A: Q.57, S.58 Ligands: MAN-MAN.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:M.56, A:S.58, A:S.58 Water bridges: A:G.7, A:G.7, A:S.55, A:S.55, A:D.59 PO4.12: 7 residues within 4Å: Chain B: D.1, I.3, Y.5 Chain D: N.2, N.18, Q.89, K.90 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:N.2, D:N.18, D:K.90, B:D.1, B:Y.5 PO4.13: 3 residues within 4Å: Chain B: K.38, I.40, R.92 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.92 Salt bridges: B:K.38, B:R.92 PO4.14: 3 residues within 4Å: Chain B: Q.57, S.58 Ligands: MAN-MAN.10 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:M.56, B:S.58, B:S.58 Water bridges: B:G.7, B:G.7, B:S.55, B:S.55, B:D.59 PO4.19: 7 residues within 4Å: Chain A: N.2, N.18, Q.89, K.90 Chain C: D.1, I.3, Y.5 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:N.2, A:N.18, A:K.90, C:D.1 PO4.20: 3 residues within 4Å: Chain C: K.38, I.40, R.92 3 PLIP interactions: 3 interactions with chain C Water bridges: C:R.92 Salt bridges: C:K.38, C:R.92 PO4.21: 3 residues within 4Å: Chain C: Q.57, S.58 Ligands: MAN-MAN.17 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:M.56, C:S.58, C:S.58 Water bridges: C:G.7, C:G.7, C:S.55, C:S.55, C:D.59 PO4.26: 7 residues within 4Å: Chain B: N.2, N.18, Q.89, K.90 Chain D: D.1, I.3, Y.5 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:N.2, B:N.18, B:K.90, D:D.1 PO4.27: 3 residues within 4Å: Chain D: K.38, I.40, R.92 3 PLIP interactions: 3 interactions with chain D Water bridges: D:R.92 Salt bridges: D:K.38, D:R.92 PO4.28: 3 residues within 4Å: Chain D: Q.57, S.58 Ligands: MAN-MAN.24 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:M.56, D:S.58, D:S.58 Water bridges: D:G.7, D:G.7, D:S.55, D:S.55, D:D.59

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sauerborn, M.K. et al., Insights into carbohydrate recognition by Narcissus pseudonarcissus lectin: the crystal structure at 2 A resolution in complex with alpha1-3 mannobiose. J.Mol.Biol. (1999)

Release Date

1998-12-23

Peptides

PROTEIN (AGGLUTININ): ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

PROTEIN (AGGLUTININ)

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