SMTL ID : 4ruq.1

Carp Fishelectin, apo form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 6 residues within 4Å: Chain A: K.11, N.25, L.26, N.27, K.45, T.59 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 6 residues within 4Å: Chain B: K.11, N.25, L.26, N.27, K.45, T.59 No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 3 residues within 4Å: Chain A: D.14, D.82, E.170 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.82, A:E.170, H2O.1, H2O.1, H2O.1 CA.7: 3 residues within 4Å: Chain B: D.14, D.82, E.170 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.82, B:E.170, H2O.7, H2O.7, H2O.7

5 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.4: 5 residues within 4Å: Chain A: G.164, L.165, L.166, Y.187, W.202 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.166, A:Y.187, A:W.202, A:W.202 Hydrogen bonds: A:L.165, A:L.165 IPA.5: 5 residues within 4Å: Chain A: G.121, K.122, L.123, F.143, F.159 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.123, A:F.143, A:F.143, A:F.159, A:F.159 Hydrogen bonds: A:K.122 IPA.8: 5 residues within 4Å: Chain B: G.8, N.9, L.10, F.30, F.37 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.10, B:F.30 Hydrogen bonds: B:N.9 IPA.9: 5 residues within 4Å: Chain B: G.164, L.165, L.166, Y.187, W.202 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.166, B:Y.187, B:W.202, B:W.202 Hydrogen bonds: B:L.165 IPA.10: 4 residues within 4Å: Chain B: L.1, M.205, L.236, T.237 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.1, B:L.1, B:M.205, B:L.236 Hydrogen bonds: B:L.1, B:T.237, B:T.237

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: G.42, S.43, N.58, F.64, F.71 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.43, A:N.58 Water bridges: A:S.41, A:S.43 GOL.11: 6 residues within 4Å: Chain B: G.42, S.43, L.44, N.58, F.64, F.71 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.43, B:S.43, B:N.58 GOL.12: 5 residues within 4Å: Chain B: G.121, K.122, N.137, F.143, F.159 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.122, B:N.137

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Capaldi, S. et al., Three-dimensional structure and ligand-binding site of carp fishelectin (FEL). Acta Crystallogr.,Sect.D (2015)

Release Date

2015-04-08

Peptides

Fish-egg lectin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Fish-egg lectin

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