SMTL ID : 4czs.1

Discovery of Glycomimetic Ligands via Genetically-encoded Library of Phage displaying Mannose-peptides

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

homo-tetramer

Ligands

4 x GLY- TRP- TYR- XSN: MAN-WYD(Non-covalent)

GLY-TRP-TYR-XSN.1: 10 residues within 4Å: Chain A: T.11, Y.12, P.13, T.15, S.21, Y.100, S.204, H.205, P.206 Ligands: 8LR.13 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.12, A:Y.12, A:P.13, A:T.15, A:H.205 Hydrogen bonds: A:T.11, A:Y.12, A:Y.12, A:Y.100, A:Y.100, A:Y.100 pi-Stacking: A:Y.100 GLY-TRP-TYR-XSN.2: 9 residues within 4Å: Chain B: T.11, Y.12, P.13, T.15, S.21, Y.100, H.205, P.206 Ligands: 8LR.14 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:Y.12, B:Y.12, B:T.15, B:H.205 Hydrogen bonds: B:T.11, B:Y.12, B:Y.12, B:Y.100, B:Y.100 Water bridges: B:Y.12 pi-Stacking: B:Y.100 GLY-TRP-TYR-XSN.3: 9 residues within 4Å: Chain C: T.11, Y.12, P.13, T.15, S.21, Y.100, H.205, P.206 Ligands: 8LR.15 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:Y.12, C:P.13, C:P.13, C:T.15, C:Y.100, C:H.205 Hydrogen bonds: C:Y.12, C:Y.100, C:Y.100, C:P.206 pi-Stacking: C:Y.100 GLY-TRP-TYR-XSN.4: 8 residues within 4Å: Chain D: T.11, Y.12, P.13, S.21, Y.100, H.205, P.206 Ligands: 8LR.16 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:Y.12, D:P.13, D:P.13, D:H.205 Hydrogen bonds: D:Y.12, D:Y.12, D:Y.12, D:Y.100, D:P.206 pi-Stacking: D:Y.100

4 x CA: CALCIUM ION(Non-covalent)

CA.5: 4 residues within 4Å: Chain A: D.10, Y.12, N.14, D.19 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.10, A:Y.12, A:D.19, H2O.4, H2O.6 CA.7: 4 residues within 4Å: Chain B: D.10, Y.12, N.14, D.19 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.10, B:D.10, B:D.19, H2O.13, H2O.13 CA.9: 4 residues within 4Å: Chain C: D.10, Y.12, N.14, D.19 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.10, C:D.10, C:Y.12, C:D.19, H2O.24 CA.11: 4 residues within 4Å: Chain D: D.10, Y.12, N.14, D.19 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.10, D:Y.12, D:D.19, H2O.31, H2O.31

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

MN.6: 4 residues within 4Å: Chain A: E.8, D.10, D.19, H.24 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.8, A:D.10, A:D.19, A:H.24, H2O.2, H2O.4 MN.8: 4 residues within 4Å: Chain B: E.8, D.10, D.19, H.24 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.8, B:D.10, B:D.19, B:H.24, H2O.13, H2O.13 MN.10: 4 residues within 4Å: Chain C: E.8, D.10, D.19, H.24 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.8, C:D.10, C:D.19, C:H.24, H2O.22, H2O.23 MN.12: 5 residues within 4Å: Chain D: E.8, D.10, D.19, H.24, S.34 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.8, D:D.10, D:D.19, D:H.24, H2O.30, H2O.30

4 x 8LR: 2-hydroxyethyl alpha-D-mannopyranoside(Non-covalent)

8LR.13: 10 residues within 4Å: Chain A: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 Ligands: GLY-TRP-TYR-XSN.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.12, A:N.14, A:L.99, A:Y.100, A:Y.100, A:D.208, A:R.228 8LR.14: 10 residues within 4Å: Chain B: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 Ligands: GLY-TRP-TYR-XSN.2 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.14, B:G.98, B:L.99, B:Y.100, B:Y.100, B:D.208, B:R.228 8LR.15: 10 residues within 4Å: Chain C: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 Ligands: GLY-TRP-TYR-XSN.3 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:N.14, C:G.98, C:L.99, C:Y.100, C:Y.100, C:D.208, C:R.228 8LR.16: 10 residues within 4Å: Chain D: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 Ligands: GLY-TRP-TYR-XSN.4 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:N.14, D:G.98, D:L.99, D:Y.100, D:Y.100, D:D.208, D:R.228

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ng, S. et al., Genetically-Encoded Fragment-Based Discovery of Glycopeptide Ligands for Carbohydrate-Binding Proteins. J.Am.Chem.Soc. (2015)

Release Date

2015-04-22

Peptides

Concanavalin V: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Concanavalin V

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