SMTL ID : 2d7f.1 (1 other biounit)

Crystal structure of A lectin from canavalia gladiata seeds complexed with alpha-methyl-mannoside and alpha-aminobutyric acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

homo-tetramer

Ligands

4 x MMA: methyl alpha-D-mannopyranoside(Non-covalent)

MMA.1: 9 residues within 4Å: Chain A: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 8 PLIP interactions: 8 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 Water bridges: A:R.228 MMA.5: 9 residues within 4Å: Chain B: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.14, B:L.99, B:Y.100, B:Y.100, B:R.228 MMA.9: 9 residues within 4Å: Chain C: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 8 PLIP interactions: 8 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 Water bridges: C:R.228 MMA.13: 9 residues within 4Å: Chain D: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:N.14, D:L.99, D:Y.100, D:Y.100, D:R.228

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

MN.2: 4 residues within 4Å: Chain A: E.8, D.10, D.19, H.24 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.8, A:D.10, A:D.19, A:H.24 MN.6: 4 residues within 4Å: Chain B: E.8, D.10, D.19, H.24 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.8, B:D.10, B:D.19, B:H.24 MN.10: 4 residues within 4Å: Chain C: E.8, D.10, D.19, H.24 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.8, C:D.10, C:D.19, C:H.24 MN.14: 4 residues within 4Å: Chain D: E.8, D.10, D.19, H.24 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.8, D:D.10, D:D.19, D:H.24

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: D.10, Y.12, N.14, D.19 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.10, A:D.10, A:Y.12, A:D.19 CA.7: 4 residues within 4Å: Chain B: D.10, Y.12, N.14, D.19 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.10, B:D.10, B:Y.12, B:D.19 CA.11: 4 residues within 4Å: Chain C: D.10, Y.12, N.14, D.19 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.10, C:D.10, C:Y.12, C:D.19 CA.15: 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

4 x DBB: D-ALPHA-AMINOBUTYRIC ACID(Non-covalent)

DBB.4: 10 residues within 4Å: Chain A: S.113, N.124, A.125, L.126, V.179, H.180 Chain B: M.129, F.130, Q.137, D.139 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:A.125, A:H.180, B:Q.137, B:D.139 DBB.8: 10 residues within 4Å: Chain A: M.129, F.130, D.139 Chain B: S.113, L.115, N.124, A.125, L.126, V.179, H.180 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.180, A:D.139 DBB.12: 10 residues within 4Å: Chain C: S.113, N.124, A.125, L.126, V.179, H.180 Chain D: M.129, F.130, Q.137, D.139 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:A.125, C:H.180, D:Q.137, D:D.139, D:D.139 DBB.16: 10 residues within 4Å: Chain C: M.129, F.130, D.139 Chain D: S.113, L.115, N.124, A.125, L.126, V.179, H.180 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:D.139, C:D.139, D:H.180

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Delatorre, P. et al., Structure of a lectin from Canavalia gladiata seeds: new structural insights for old molecules. Bmc Struct.Biol. (2007)

Release Date

2006-12-19

Peptides

Concanavalin A: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
S

C
A

D
S

Concanavalin A

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