SMTL ID : 6tt9.1

rTBL Recombinant Lectin From Tepary Bean

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

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

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.1: 11 residues within 4Å: Chain A: R.17, F.18, N.19, E.20, S.32, S.33, G.35 Chain B: S.67, K.122, E.208, W.209 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Non-functional Binders)

NAG-NAG.2: 8 residues within 4Å: Chain A: E.208, W.209 Chain B: R.17, F.18, N.19, E.20, V.31, S.32 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 10 residues within 4Å: Chain C: R.17, F.18, N.19, E.20, V.31, S.32 Chain D: S.67, T.68, E.208, W.209 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.67

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-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(Non-functional Binders)

NAG-NAG-BMA-MAN-MAN-MAN.4: 8 residues within 4Å: Chain C: E.208, W.209 Chain D: R.17, F.18, N.19, E.20, S.32, S.33 No protein-ligand interaction detected (PLIP)

4 x CA: CALCIUM ION(Non-functional Binders)(Non-covalent)

CA.5: 4 residues within 4Å: Chain A: D.131, L.133, N.135, D.139 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.131, A:D.131, A:L.133, A:D.139, H2O.2 CA.8: 4 residues within 4Å: Chain B: D.131, L.133, N.135, D.139 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.131, B:L.133, B:D.139, H2O.6, H2O.7 CA.11: 4 residues within 4Å: Chain C: D.131, L.133, N.135, D.139 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.131, C:L.133, C:D.139, H2O.12, H2O.13 CA.15: 4 residues within 4Å: Chain D: D.131, L.133, N.135, D.139 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.131, D:D.131, D:L.133, D:D.139, H2O.17

4 x MN: MANGANESE (II) ION(Non-covalent)(Post Translational Modification)

MN.6: 4 residues within 4Å: Chain A: E.129, D.131, D.139, H.144 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.129, A:D.131, A:D.139, A:H.144, H2O.1, H2O.2 MN.9: 4 residues within 4Å: Chain B: E.129, D.131, D.139, H.144 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.129, B:D.131, B:D.139, B:H.144, H2O.6, H2O.7 MN.12: 4 residues within 4Å: Chain C: E.129, D.131, D.139, H.144 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.129, C:D.131, C:D.139, C:H.144, H2O.11, H2O.11 MN.16: 4 residues within 4Å: Chain D: E.129, D.131, D.139, H.144 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.129, D:D.131, D:D.139, D:H.144, H2O.16, H2O.17

5 x HEX: HEXANE(Non-functional Binders)(Non-covalent)(Post Translational Modification)

HEX.7: 3 residues within 4Å: Chain A: S.74, F.75, Y.174 No protein-ligand interaction detected (PLIP) HEX.10: 5 residues within 4Å: Chain B: S.74, F.75, Y.174, A.236, K.238 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:K.238 HEX.13: 5 residues within 4Å: Chain C: S.74, F.75, A.76, Y.174, A.236 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:A.76 HEX.14: 3 residues within 4Å: Chain C: A.76, S.78, L.171 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.171 HEX.17: 5 residues within 4Å: Chain D: S.74, F.75, T.173, Y.174, A.236 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Martinez-Alarcon, D. et al., Recombinant Lectin from Tepary Bean (Phaseolus acutifolius) with Specific Recognition for Cancer-Associated Glycans: Production, Structural Characterization, and Target Identification. Biomolecules (2020)

Release Date

2020-05-13

Peptides

Phytohemagglutinin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

C
CCC

D
DDD

Phytohemagglutinin