SMTL ID : 1hql.1

The xenograft antigen in complex with the B4 isolectin of Griffonia simplicifolia lectin-1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

4 x MBG- GLA: alpha-D-galactopyranose-(1-3)-methyl beta-D-galactopyranoside(Non-covalent)(Post Translational Modification)

MBG-GLA.1: 10 residues within 4Å: Chain A: W.47, A.87, D.88, G.105, E.106, W.132, N.134, G.221, N.222, N.223 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.88, A:E.106, A:E.106, A:N.134, A:G.221, A:N.222, A:N.222, A:N.223, A:N.223, A:N.222 MBG-GLA.3: 10 residues within 4Å: Chain B: W.47, A.87, D.88, G.105, E.106, W.132, N.134, G.221, N.222, N.223 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.88, B:E.106, B:E.106, B:N.134, B:N.222, B:N.222, B:N.223, B:N.223 Water bridges: B:E.106, B:N.136 MBG-GLA.9: 10 residues within 4Å: Chain C: W.47, A.87, D.88, G.105, E.106, W.132, N.134, G.221, N.222, N.223 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.88, C:E.106, C:E.106, C:N.134, C:G.221, C:N.222, C:N.222, C:N.223, C:N.223, C:N.222 MBG-GLA.11: 10 residues within 4Å: Chain D: W.47, A.87, D.88, G.105, E.106, W.132, N.134, G.221, N.222, N.223 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.88, D:E.106, D:E.106, D:N.134, D:N.222, D:N.222, D:N.223, D:N.223 Water bridges: D:E.106, D:N.136

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

NAG-NAG.2: 4 residues within 4Å: Chain A: E.17, F.22, N.27 Chain B: Y.41 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: Y.41, T.82 Chain B: N.27 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.82 Hydrogen bonds: A:Y.41 NAG-NAG.10: 4 residues within 4Å: Chain C: E.17, F.22, N.27 Chain D: Y.41 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain C: Y.41, T.82 Chain D: N.27 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:T.82 Hydrogen bonds: C:Y.41

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

MN.5: 4 residues within 4Å: Chain A: E.128, D.130, E.139, H.144 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.128, A:D.130, A:E.139, A:H.144, H2O.1, H2O.1 MN.7: 4 residues within 4Å: Chain B: E.128, D.130, E.139, H.144 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.128, B:D.130, B:E.139, B:H.144, H2O.2, H2O.3 MN.13: 4 residues within 4Å: Chain C: E.128, D.130, E.139, H.144 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.128, C:D.130, C:E.139, C:H.144, H2O.5, H2O.5 MN.15: 4 residues within 4Å: Chain D: E.128, D.130, E.139, H.144 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.128, D:D.130, D:E.139, D:H.144, H2O.7, H2O.7

4 x CA: CALCIUM ION(Non-covalent)

CA.6: 4 residues within 4Å: Chain A: D.130, W.132, N.134, E.139 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.130, A:W.132, A:E.139, H2O.1, H2O.1 CA.8: 4 residues within 4Å: Chain B: D.130, W.132, N.134, E.139 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.130, B:W.132, B:E.139, H2O.2, H2O.3 CA.14: 4 residues within 4Å: Chain C: D.130, W.132, N.134, E.139 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.130, C:W.132, C:E.139, H2O.5, H2O.5 CA.16: 4 residues within 4Å: Chain D: D.130, W.132, N.134, E.139 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.130, D:W.132, D:E.139, H2O.7, H2O.7

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Tempel, W. et al., The xenograft antigen bound to Griffonia simplicifolia lectin 1-B(4). X-ray crystal structure of the complex and molecular dynamics characterization of the binding site. J.Biol.Chem. (2002)

Release Date

2002-01-16

Peptides

LECTIN: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

LECTIN

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