SMTL ID : 3a0d.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x MMA: methyl alpha-D-mannopyranoside(Non-covalent)

MMA.1: 7 residues within 4Å: Chain A: Q.90, D.92, N.94, Y.98 Chain B: H.84, V.101, A.104 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.90, A:N.94, A:Y.98 Water bridges: B:S.6, B:Y.85 Salt bridges: B:H.84 MMA.7: 7 residues within 4Å: Chain A: H.84, V.101, A.104 Chain B: Q.90, D.92, N.94, Y.98 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Water bridges: A:S.6, A:Y.85 Salt bridges: A:H.84 Hydrogen bonds: B:Q.90, B:N.94, B:Y.98, B:Y.98

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: 3 residues within 4Å: Chain A: P.7, N.59, H.84 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.59, A:N.59 Salt bridges: A:H.84 SO4.4: 4 residues within 4Å: Chain A: E.17, V.18, G.19 Chain B: V.1 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.15 Water bridges: A:R.23 Salt bridges: A:H.14 SO4.6: 3 residues within 4Å: Chain A: K.39, V.41, R.93 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.93 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: 3 residues within 4Å: Chain B: P.7, N.59, H.84 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.59, B:N.59 Salt bridges: B:H.84 SO4.10: 4 residues within 4Å: Chain A: V.1 Chain B: E.17, V.18, G.19 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:V.1, B:G.19 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 Water bridges: B:R.23 Salt bridges: B:H.14 SO4.12: 3 residues within 4Å: Chain B: K.39, V.41, R.93 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.93 Salt bridges: B:K.39, B:R.93

Links

RCSB   PDBe   PDBe-KB   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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