SMTL ID : 7exo.1

Structure of legume lectin domain from Methanocaldococcus jannaschii in mannose bound form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.1: 4 residues within 4Å: Chain A: Y.136, L.168, S.169, L.170 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.136 Hydrogen bonds: A:S.169 MPD.4: 3 residues within 4Å: Chain A: V.152, Q.161, Y.163 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.152 Water bridges: A:Y.163, A:Y.163

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

BMA.2: 9 residues within 4Å: Chain A: A.62, D.63, G.81, G.82, W.100, N.102, G.193, G.194, A.195 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.82, A:G.193, A:G.194, A:A.195, A:A.195

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 4 residues within 4Å: Chain A: P.40, S.71, S.183, Y.185 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.183

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: P.3, I.4, P.203, I.204, Y.205 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.3 Water bridges: A:N.5, A:V.206, A:V.206 GOL.6: 4 residues within 4Å: Chain A: N.102, D.103, A.106, A.108 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.103, A:A.108

1 x CA: CALCIUM ION(Non-covalent)

CA.7: 4 residues within 4Å: Chain A: D.98, W.100, N.102, D.105 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.98, A:D.98, A:W.100, A:D.105, H2O.2

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.8: 5 residues within 4Å: Chain A: E.96, D.98, D.105, H.112, H.123 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.96, A:D.98, A:D.105, A:H.112, A:H.123, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Khan, F. et al., Crystal structure of an L-type lectin domain from archaea. Proteins (2023)

Release Date

2022-06-01

Peptides

Legume lectin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Legume lectin

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