SMTL ID : 3dzw.1 (2 other biounits)

Structure of Narcissus pseudonarcissus lectin complex with Mannobiose at 1.7 A resolution, form II

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

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

MAN-MAN.1: 7 residues within 4Å: Chain A: Q.89, D.91, N.93, Y.97 Chain B: N.83, N.107 Ligands: PO4.4 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.89, A:D.91, A:N.93, A:Y.97, A:Y.97 Water bridges: B:N.83 MAN-MAN.2: 8 residues within 4Å: Chain A: Q.26, D.28, N.30, Y.34, P.39 Chain D: D.37, K.38 Ligands: PO4.5 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain D Water bridges: A:Q.26, A:Y.34, D:K.38 Hydrogen bonds: D:D.37, D:K.38 MAN-MAN.3: 6 residues within 4Å: Chain A: Q.57, D.59, N.61, Y.65, P.71, A.74 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.59 MAN-MAN.7: 7 residues within 4Å: Chain A: N.83, N.107 Chain B: Q.89, D.91, N.93, Y.97 Ligands: PO4.10 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.89, B:D.91, B:N.93, B:Y.97 Water bridges: A:N.83 MAN-MAN.8: 8 residues within 4Å: Chain B: Q.26, D.28, N.30, Y.34, P.39 Chain C: D.37, K.38 Ligands: PO4.11 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain C Water bridges: B:Q.26, B:D.28, B:Y.34, C:K.38 Hydrogen bonds: C:D.37, C:K.38 MAN-MAN.9: 6 residues within 4Å: Chain B: Q.57, D.59, N.61, Y.65, P.71, A.74 No protein-ligand interaction detected (PLIP) MAN-MAN.13: 8 residues within 4Å: Chain C: Q.89, D.91, N.93, Y.97 Chain D: N.83, A.103, N.107 Ligands: PO4.17 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.89, C:D.91, C:N.93, C:Y.97, C:Y.97 MAN-MAN.14: 7 residues within 4Å: Chain B: D.37, K.38 Chain C: Q.26, D.28, N.30, Y.34 Ligands: PO4.16 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:D.37, B:K.38 Water bridges: B:K.38, B:K.38, C:Y.34 MAN-MAN.15: 5 residues within 4Å: Chain C: Q.57, D.59, N.61, Y.65, P.71 1 PLIP interactions: 1 interactions with chain C Water bridges: C:D.59 MAN-MAN.18: 8 residues within 4Å: Chain C: N.83, A.103, N.107 Chain D: Q.89, D.91, N.93, Y.97 Ligands: PO4.22 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.89, D:D.91, D:N.93, D:Y.97 MAN-MAN.19: 7 residues within 4Å: Chain A: D.37, K.38 Chain D: Q.26, D.28, N.30, Y.34 Ligands: PO4.21 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:D.37, A:K.38 Water bridges: A:K.38, D:Y.34, D:Y.34 MAN-MAN.20: 5 residues within 4Å: Chain D: Q.57, D.59, N.61, Y.65, P.71 No protein-ligand interaction detected (PLIP)

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

PO4.4: 4 residues within 4Å: Chain A: D.91 Chain B: Y.5, E.8 Ligands: MAN-MAN.1 No protein-ligand interaction detected (PLIP) PO4.5: 5 residues within 4Å: Chain A: P.39, I.40, W.41, A.42 Ligands: MAN-MAN.2 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.42 PO4.6: 4 residues within 4Å: Chain A: D.1, N.2 Chain B: N.2 Ligands: PO4.12 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.2, A:N.2, A:N.2 Water bridges: A:D.1, B:N.18 PO4.10: 4 residues within 4Å: Chain A: Y.5, E.8 Chain B: D.91 Ligands: MAN-MAN.7 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.91, A:E.8 PO4.11: 5 residues within 4Å: Chain B: P.39, I.40, W.41, A.42 Ligands: MAN-MAN.8 1 PLIP interactions: 1 interactions with chain B Water bridges: B:A.42 PO4.12: 4 residues within 4Å: Chain A: N.2 Chain B: D.1, N.2 Ligands: PO4.6 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.2, B:N.2, B:N.2 Water bridges: A:N.18 PO4.16: 4 residues within 4Å: Chain C: P.39, W.41, A.42 Ligands: MAN-MAN.14 No protein-ligand interaction detected (PLIP) PO4.17: 4 residues within 4Å: Chain C: D.91 Chain D: Y.5, E.8 Ligands: MAN-MAN.13 3 PLIP interactions: 3 interactions with chain D Water bridges: D:S.6, D:N.83, D:N.83 PO4.21: 4 residues within 4Å: Chain D: P.39, W.41, A.42 Ligands: MAN-MAN.19 No protein-ligand interaction detected (PLIP) PO4.22: 4 residues within 4Å: Chain C: Y.5, E.8 Chain D: D.91 Ligands: MAN-MAN.18 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:E.8, D:D.91 Water bridges: C:S.6, C:N.83, C:N.83

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rizkallah, P.J. et al., Structure of Narcissus pseudonarcissus lectin complex with Mannobiose at 1.7 A resolution, form II. To be Published

Release Date

2009-08-11

Peptides

Agglutinin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
B

D
B

Agglutinin

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