SMTL ID : 8a9m.1

Hippeastrum hybrid agglutinin, HHA, complex with beta-mannose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

4 x BMA: beta-D-mannopyranose(Non-covalent)

BMA.1: 9 residues within 4Å: Chain A: N.83, A.100, A.103, N.107 Chain B: Q.89, D.91, N.93, V.95, Y.97 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.89, B:D.91, B:N.93, B:Y.97 Water bridges: A:Y.84, A:N.107 BMA.5: 9 residues within 4Å: Chain A: Q.89, D.91, N.93, V.95, Y.97 Chain B: N.83, A.100, A.103, N.107 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.89, A:D.91, A:N.93, A:Y.97, A:Y.97 Water bridges: B:Y.84, B:N.107 BMA.9: 7 residues within 4Å: Chain C: N.83, A.103, N.107 Chain D: Q.89, D.91, N.93, Y.97 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:Q.89, D:D.91, D:N.93, D:Y.97 Water bridges: C:Y.84, C:N.107 BMA.12: 7 residues within 4Å: Chain C: Q.89, D.91, N.93, Y.97 Chain D: N.83, A.103, N.107 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Q.89, C:D.91, C:N.93, C:Y.97, C:Y.97 Water bridges: D:Y.84, D:N.107

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

PO4.2: 5 residues within 4Å: Chain A: N.81, G.82, N.83, T.99, A.100 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.83, A:N.83, A:A.100, A:A.100 PO4.3: 6 residues within 4Å: Chain A: S.6, G.7, S.55, M.56, Q.57, S.58 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.7, A:S.55, A:S.55, A:S.58 PO4.4: 12 residues within 4Å: Chain A: N.17, G.19, P.20, Y.21, T.22, V.36 Chain D: N.17, G.19, P.20, Y.21, T.22, V.36 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:N.17, D:T.22, D:T.22, D:V.36, A:G.19, A:P.20, A:T.22 PO4.6: 5 residues within 4Å: Chain B: N.81, G.82, N.83, T.99, A.100 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.83, B:N.83, B:T.99, B:A.100, B:A.100 PO4.7: 6 residues within 4Å: Chain B: S.6, G.7, S.55, M.56, Q.57, S.58 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.7, B:S.55, B:S.55, B:S.58 PO4.8: 12 residues within 4Å: Chain B: N.17, G.19, P.20, Y.21, T.22, V.36 Chain C: N.17, G.19, P.20, Y.21, T.22, V.36 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:N.17, C:T.22, C:T.22, C:V.36, B:G.19, B:P.20, B:T.22 PO4.10: 4 residues within 4Å: Chain C: G.82, N.83, T.99, A.100 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.83, C:N.83, C:A.100, C:A.100, C:A.100 PO4.11: 5 residues within 4Å: Chain C: G.13, I.24, M.25, Q.26, Q.27 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.27 PO4.13: 4 residues within 4Å: Chain D: G.82, N.83, T.99, A.100 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:N.83, D:N.83, D:T.99, D:A.100, D:A.100, D:A.100 PO4.14: 5 residues within 4Å: Chain D: G.13, I.24, M.25, Q.26, Q.27 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.27

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chantalat, L. et al., X-ray structure solution of amaryllis lectin by molecular replacement with only 4% of the total diffracting matter. Acta Crystallogr D Biol Crystallogr (1996)

Release Date

2022-10-05

Peptides

Agglutinin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
B

D
B

Agglutinin