SMTL ID : 3d4k.1

Concanavalin A Complexed to a Synthetic Analog of the Trimannoside

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

4 x H1M- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]methyl 2-deoxy-2-(2-hydroxyethyl)-alpha-D-mannopyranoside

H1M-MAN-MAN.1: 12 residues within 4Å: Chain A: Y.12, P.13, N.14, T.15, D.16, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.12, A:R.228, A:N.14, A:G.98, A:L.99, A:Y.100, A:Y.100, A:R.228 Water bridges: A:R.228 H1M-MAN-MAN.2: 12 residues within 4Å: Chain B: Y.12, P.13, N.14, T.15, D.16, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.12, B:D.16, B:N.14, B:G.98, B:L.99, B:Y.100, B:Y.100, B:R.228 Water bridges: B:Y.12, B:R.228, B:R.228, B:R.228 H1M-MAN-MAN.9: 12 residues within 4Å: Chain C: Y.12, P.13, N.14, T.15, D.16, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Y.12, C:Y.12, C:N.14, C:G.98, C:L.99, C:Y.100, C:Y.100, C:R.228 Water bridges: C:D.16, C:R.228, C:R.228, C:R.228 H1M-MAN-MAN.10: 12 residues within 4Å: Chain D: Y.12, P.13, N.14, T.15, D.16, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:Y.12, D:Y.12, D:N.14, D:G.98, D:L.99, D:Y.100, D:Y.100, D:R.228 Water bridges: D:R.228, D:R.228

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

MN.3: 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.2 MN.6: 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.6, H2O.6 MN.11: 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.12, H2O.13 MN.14: 4 residues within 4Å: Chain D: E.8, D.10, D.19, H.24 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.18, H2O.19

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 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.1, H2O.2 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:Y.12, B:D.19, H2O.6, H2O.8 CA.12: 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.12, H2O.14 CA.15: 4 residues within 4Å: Chain D: D.10, Y.12, N.14, D.19 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.10, D:D.10, D:Y.12, D:D.19, H2O.18

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain A: S.113, N.124, A.125, V.179, H.180 Chain B: F.130, Q.137, D.139 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.113, A:S.113, A:H.180, B:Q.137, B:D.139 Water bridges: A:N.124 GOL.8: 8 residues within 4Å: Chain A: F.130, D.139 Chain B: S.113, K.114, L.115, N.124, V.179, H.180 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.180 Water bridges: B:K.114, B:H.180, A:Q.137 GOL.13: 8 residues within 4Å: Chain C: S.113, L.115, N.124, V.179, H.180 Chain D: F.130, Q.137, D.139 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:Q.137, D:D.139, D:D.139, C:S.113, C:S.113, C:H.180 Water bridges: C:N.124 GOL.16: 9 residues within 4Å: Chain C: F.130, Q.137, D.139 Chain D: S.113, N.124, A.125, L.126, V.179, H.180 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Q.137, C:D.139, D:N.124, D:H.180

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kadirvelraj, R. et al., Involvement of water in carbohydrate-protein binding: concanavalin A revisited. J.Am.Chem.Soc. (2008)

Release Date

2009-03-03

Peptides

Concanavalin-A: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
B

D
C

Concanavalin-A

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