SMTL ID : 7elv.1

Structure of legume lectin domain from Methanocaldococcus jannaschii in apo form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

3 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.2: 6 residues within 4Å: Chain A: G.13, N.14, G.30, A.32, L.77, T.80 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.32, A:L.77, A:T.80 Hydrogen bonds: A:N.14, A:N.14 MPD.3: 6 residues within 4Å: Chain A: P.3, I.4, W.9, P.203, I.204, Y.205 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.9 Hydrogen bonds: A:P.203 Water bridges: A:V.206

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 9 residues within 4Å: Chain A: A.62, D.63, G.81, G.82, W.100, N.102, G.193, G.194, A.195 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.82, A:N.102, A:G.193, A:G.194, A:A.195, A:A.195 Water bridges: A:T.80, A:G.194 GOL.5: 5 residues within 4Å: Chain A: P.40, S.71, S.183, A.184, Y.185 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.185, A:Y.185, A:Y.185

1 x CA: CALCIUM ION(Non-covalent)

CA.6: 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.7: 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

2022-04-20

Peptides

legume lectin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

legume lectin

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