SMTL ID : 1tei.3 (2 other biounits)

STRUCTURE OF CONCANAVALIN A COMPLEXED TO BETA-D-GLCNAC (1,2)ALPHA-D-MAN-(1,6)[BETA-D-GLCNAC(1,2)ALPHA-D-MAN (1,6)]ALPHA-D-MAN

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-octamer

Ligands

8 x MAN- MAN- NAG- MAN- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose

MAN-MAN-NAG-MAN-NAG.1: 17 residues within 4Å: Chain A: Y.12, P.13, N.14, T.15, D.16, G.98, L.99, Y.100, S.168, H.205, A.207, D.208, G.224, T.226, G.227, R.228, L.229 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.14, A:N.14, A:G.98, A:L.99, A:Y.100, A:Y.100, A:R.228, A:R.228, A:S.168, A:T.226, A:T.226, A:L.229 MAN-MAN-NAG-MAN-NAG.2: 17 residues within 4Å: Chain B: Y.12, P.13, N.14, T.15, D.16, G.98, L.99, Y.100, S.168, H.205, A.207, D.208, G.224, T.226, G.227, R.228, L.229 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.14, B:G.98, B:L.99, B:Y.100, B:Y.100, B:R.228, B:R.228, B:S.168, B:T.226, B:T.226 MAN-MAN-NAG-MAN-NAG.3: 17 residues within 4Å: Chain C: Y.12, P.13, N.14, T.15, D.16, G.98, L.99, Y.100, S.168, H.205, A.207, D.208, G.224, T.226, G.227, R.228, L.229 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.14, C:N.14, C:G.98, C:L.99, C:Y.100, C:Y.100, C:R.228, C:R.228, C:S.168, C:T.226, C:T.226, C:L.229 MAN-MAN-NAG-MAN-NAG.4: 18 residues within 4Å: Chain D: Y.12, P.13, N.14, T.15, D.16, T.97, G.98, L.99, Y.100, S.168, H.205, A.207, D.208, G.224, T.226, G.227, R.228, L.229 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:N.14, D:G.98, D:L.99, D:Y.100, D:Y.100, D:R.228, D:R.228, D:S.168, D:T.226, D:T.226, D:R.228, D:L.229 MAN-MAN-NAG-MAN-NAG.5: 17 residues within 4Å: Chain E: Y.12, P.13, N.14, T.15, D.16, G.98, L.99, Y.100, S.168, H.205, A.207, D.208, G.224, T.226, G.227, R.228, L.229 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:N.14, E:G.98, E:L.99, E:Y.100, E:Y.100, E:R.228, E:R.228, E:S.168, E:T.226, E:T.226, E:L.229 MAN-MAN-NAG-MAN-NAG.6: 17 residues within 4Å: Chain F: Y.12, P.13, N.14, T.15, D.16, G.98, L.99, Y.100, S.168, H.205, A.207, D.208, G.224, T.226, G.227, R.228, L.229 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:N.14, F:G.98, F:L.99, F:Y.100, F:Y.100, F:R.228, F:R.228, F:S.168, F:T.226, F:T.226, F:R.228 MAN-MAN-NAG-MAN-NAG.7: 17 residues within 4Å: Chain G: Y.12, P.13, N.14, T.15, D.16, G.98, L.99, Y.100, S.168, H.205, A.207, D.208, G.224, T.226, G.227, R.228, L.229 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:N.14, G:N.14, G:G.98, G:L.99, G:Y.100, G:Y.100, G:R.228, G:R.228, G:S.168, G:T.226, G:T.226 MAN-MAN-NAG-MAN-NAG.8: 17 residues within 4Å: Chain H: Y.12, P.13, N.14, T.15, D.16, G.98, L.99, Y.100, S.168, H.205, A.207, D.208, G.224, T.226, G.227, R.228, L.229 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:N.14, H:N.14, H:G.98, H:L.99, H:Y.100, H:Y.100, H:R.228, H:T.226, H:T.226, H:L.229

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

MN.9: 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.1, H2O.1 MN.11: 5 residues within 4Å: Chain B: E.8, D.10, D.19, H.24 Ligands: CA.12 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.1, H2O.1 MN.13: 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.2, H2O.2 MN.15: 4 residues within 4Å: Chain D: E.8, D.10, D.19, H.24 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.8, D:D.10, D:D.19, D:H.24, H2O.2 MN.17: 4 residues within 4Å: Chain E: E.8, D.10, D.19, H.24 6 PLIP interactions: 4 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.8, E:D.10, E:D.19, E:H.24, H2O.2, H2O.2 MN.19: 5 residues within 4Å: Chain F: E.8, D.10, D.19, H.24, S.34 6 PLIP interactions: 4 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.8, F:D.10, F:D.19, F:H.24, H2O.3, H2O.3 MN.21: 5 residues within 4Å: Chain G: E.8, D.10, D.19, H.24, S.34 6 PLIP interactions: 4 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:E.8, G:D.10, G:D.19, G:H.24, H2O.3, H2O.3 MN.23: 5 residues within 4Å: Chain H: E.8, D.10, D.19, H.24, S.34 5 PLIP interactions: 4 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:E.8, H:D.10, H:D.19, H:H.24, H2O.3

8 x CA: CALCIUM ION(Non-covalent)

CA.10: 4 residues within 4Å: Chain A: D.10, Y.12, N.14, D.19 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.10, A:D.10, A:Y.12, A:D.19, H2O.1 CA.12: 5 residues within 4Å: Chain B: D.10, Y.12, N.14, D.19 Ligands: MN.11 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.10, B:Y.12, B:D.19, H2O.1, H2O.1 CA.14: 4 residues within 4Å: Chain C: D.10, Y.12, N.14, D.19 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.10, C:Y.12, C:D.19, H2O.1, H2O.2 CA.16: 4 residues within 4Å: Chain D: D.10, Y.12, N.14, D.19 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.10, D:D.10, D:Y.12, D:D.19 CA.18: 4 residues within 4Å: Chain E: D.10, Y.12, N.14, D.19 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.10, E:Y.12, E:D.19, H2O.2, H2O.3 CA.20: 4 residues within 4Å: Chain F: D.10, Y.12, N.14, D.19 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.10, F:D.10, F:Y.12, F:D.19 CA.22: 4 residues within 4Å: Chain G: D.10, Y.12, N.14, D.19 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:D.10, G:Y.12, G:D.19, H2O.3, H2O.3 CA.24: 5 residues within 4Å: Chain H: D.10, Y.12, P.13, N.14, D.19 5 PLIP interactions: 4 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.10, H:D.10, H:Y.12, H:D.19, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Moothoo, D.N. et al., Concanavalin A distorts the beta-GlcNAc-(1-->2)-Man linkage of beta-GlcNAc-(1-->2)-alpha-Man-(1-->3)-[beta-GlcNAc-(1-->2)-alpha-Man- (1-->6)]-Man upon binding. Glycobiology (1998)

Release Date

1997-08-20

Peptides

CONCANAVALIN A: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

CONCANAVALIN A

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