SMTL ID : 1zhs.1 (3 other biounits)

Crystal structure of MVL bound to Man3GlcNAc2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

4 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.1: 15 residues within 4Å: Chain A: P.11, L.12, W.13, S.14, N.15, Q.19, G.35, Q.36, W.37, T.38, T.39, E.42, S.43, S.46 Ligands: EDO.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.36, A:W.37, A:Q.36, A:N.15, A:T.38, A:T.38, A:T.39 Water bridges: A:Q.36, A:N.15, A:N.15, A:A.16 NAG-NAG-BMA-MAN-MAN.2: 15 residues within 4Å: Chain A: P.70, L.71, W.72, S.73, N.74, Q.78, G.94, Q.95, W.96, R.97, T.98, E.101, G.102, S.105 Ligands: EDO.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.95, A:W.96, A:Q.95, A:N.74, A:T.98 Water bridges: A:Q.95, A:N.74, A:N.74, A:D.75 NAG-NAG-BMA-MAN-MAN.3: 14 residues within 4Å: Chain B: P.11, L.12, W.13, S.14, N.15, Q.19, G.35, Q.36, W.37, T.38, T.39, E.42, S.43, A.44 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.15, B:Q.36, B:W.37, B:N.15, B:Q.36, B:N.15, B:T.38, B:T.39, B:T.39 Water bridges: B:Q.36, B:N.15, B:N.15, B:A.16 NAG-NAG-BMA-MAN-MAN.4: 15 residues within 4Å: Chain B: P.70, L.71, W.72, S.73, N.74, Q.78, G.94, Q.95, W.96, R.97, T.98, E.101, G.102, S.105 Ligands: EDO.11 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.95, B:W.96, B:N.74, B:Q.95, B:N.74, B:T.98, B:T.98 Water bridges: B:D.75

7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 5 residues within 4Å: Chain A: D.65, Q.95, W.96, R.97 Ligands: NAG-NAG-BMA-MAN-MAN.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.65, A:R.97, A:R.97 Water bridges: A:R.97 EDO.6: 7 residues within 4Å: Chain A: N.6, Q.36, W.37, T.38, E.49 Ligands: NAG-NAG-BMA-MAN-MAN.1, EDO.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.6 EDO.7: 6 residues within 4Å: Chain A: K.4, V.5, N.6, E.49 Chain B: N.6 Ligands: EDO.6 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.6, A:E.49, A:E.49, B:N.6 Water bridges: A:N.6 EDO.8: 5 residues within 4Å: Chain A: H.29, L.52, S.87, Y.88 Chain B: P.8 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.29, A:S.87 Water bridges: A:H.29, A:Y.88, A:Y.88 EDO.9: 6 residues within 4Å: Chain B: Q.30, G.31, N.32, E.51, L.52, Q.53 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.51, B:Q.53 EDO.10: 5 residues within 4Å: Chain A: P.8 Chain B: H.29, L.52, S.87, Y.88 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B Water bridges: A:Y.88, B:A.28, B:H.29, B:H.29, B:Y.88 Hydrogen bonds: B:S.87 EDO.11: 6 residues within 4Å: Chain B: D.65, Q.95, W.96, R.97, Q.108 Ligands: NAG-NAG-BMA-MAN-MAN.4 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.65, B:R.97

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Williams, D.C. et al., Crystal Structures of the HIV-1 Inhibitory Cyanobacterial Protein MVL Free and Bound to Man3GlcNAc2: STRUCTURAL BASIS FOR SPECIFICITY AND HIGH-AFFINITY BINDING TO THE CORE PENTASACCHARIDE FROM N-LINKED OLIGOMANNOSIDE. J.Biol.Chem. (2005)

Release Date

2005-06-07

Peptides

mannan-binding lectin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

mannan-binding lectin

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