SMTL ID : 3a0e.1

Crystal Structure of Polygonatum cyrtonema lectin (PCL) complexed with dimannoside

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

MAN-MAN.1: 8 residues within 4Å: Chain A: Q.90, D.92, N.94, Y.98 Chain B: H.84, V.101, A.104 Ligands: SO4.9 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Water bridges: B:Y.85 Hydrogen bonds: A:Q.90, A:D.92, A:N.94, A:Y.98 MAN-MAN.7: 8 residues within 4Å: Chain A: H.84, V.101, A.104 Chain B: Q.90, D.92, N.94, Y.98 Ligands: SO4.3 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.90, B:D.92, B:N.94, B:Y.98, B:Y.98 Water bridges: A:Y.85

10 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: Q.27, D.29, N.31, Y.35, G.47 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.27, A:N.31, A:Y.35 SO4.3: 4 residues within 4Å: Chain A: P.7, N.59, H.84 Ligands: MAN-MAN.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.59, A:N.59 Salt bridges: A:H.84 SO4.4: 5 residues within 4Å: Chain A: E.17, V.18, G.19 Chain B: V.1 Ligands: SO4.10 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:V.1, A:G.19 SO4.5: 2 residues within 4Å: Chain A: H.14, S.15 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.15, A:S.15 Water bridges: A:H.14 Salt bridges: A:H.14 SO4.6: 3 residues within 4Å: Chain A: K.39, V.41, R.93 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.39, A:R.93 SO4.8: 5 residues within 4Å: Chain B: Q.27, D.29, N.31, Y.35, G.47 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.27, B:N.31, B:Y.35 SO4.9: 4 residues within 4Å: Chain B: P.7, N.59, H.84 Ligands: MAN-MAN.1 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.59, B:N.59 Salt bridges: B:H.84 SO4.10: 5 residues within 4Å: Chain A: V.1 Chain B: E.17, V.18, G.19 Ligands: SO4.4 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.19, A:V.1 Water bridges: B:V.1, B:V.1, B:V.1 SO4.11: 2 residues within 4Å: Chain B: H.14, S.15 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.15, B:S.15 Salt bridges: B:H.14 SO4.12: 3 residues within 4Å: Chain B: K.39, V.41, R.93 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.39, B:R.93

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Ding, J. et al., Crystal structures of a novel anti-HIV mannose-binding lectin from Polygonatum cyrtonema Hua with unique ligand-binding property and super-structure. J.Struct.Biol. (2010)

Release Date

2010-03-16

Peptides

Mannose/sialic acid-binding lectin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Mannose/sialic acid-binding lectin

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