SMTL ID : 4i30.1

Crystal structure of Canavalia maritima seeds lectin (ConM) co-crystalized with gamma-aminobutyric acid (GABA) and soaked with adenine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-tetramer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 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.4 CA.5: 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.7, H2O.7 CA.9: 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.10, H2O.10 CA.13: 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.14, H2O.14

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

MN.2: 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.4, H2O.4 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.7, H2O.7 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.10, H2O.11 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.14, H2O.14

4 x ABU: GAMMA-AMINO-BUTANOIC ACID(Non-covalent)

ABU.3: 10 residues within 4Å: Chain A: S.113, K.114, L.115, N.124, A.125, L.126, V.179, H.180 Chain D: F.130, D.139 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:L.115, A:H.180 Hydrogen bonds: A:H.180, A:H.180 Water bridges: D:Q.137 ABU.7: 10 residues within 4Å: Chain B: S.113, K.114, L.115, N.124, A.125, L.126, V.179, H.180 Chain C: F.130, D.139 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:L.115, B:H.180 Hydrogen bonds: B:H.180, B:H.180 Water bridges: C:Q.137 ABU.11: 10 residues within 4Å: Chain B: F.130, D.139 Chain C: S.113, K.114, L.115, N.124, A.125, L.126, V.179, H.180 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:L.115, C:H.180 Hydrogen bonds: C:H.180, C:H.180, B:D.139 Water bridges: B:Q.137 ABU.15: 10 residues within 4Å: Chain A: F.130, D.139 Chain D: S.113, K.114, L.115, N.124, A.125, L.126, V.179, H.180 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain D Hydrogen bonds: A:D.139, D:H.180, D:H.180 Water bridges: A:Q.137 Hydrophobic interactions: D:L.115, D:H.180

4 x ADE: ADENINE(Non-covalent)

ADE.4: 6 residues within 4Å: Chain A: Y.12, P.13, N.14, T.15, D.16, R.228 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.12, A:N.14, A:D.16, A:D.16, A:R.228 ADE.8: 6 residues within 4Å: Chain B: Y.12, P.13, N.14, T.15, D.16, R.228 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.12, B:N.14, B:D.16, B:D.16, B:R.228 ADE.12: 6 residues within 4Å: Chain C: Y.12, P.13, N.14, T.15, D.16, R.228 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Y.12, C:Y.12, C:N.14, C:D.16, C:R.228 ADE.16: 6 residues within 4Å: Chain D: Y.12, P.13, N.14, T.15, D.16, R.228 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Y.12, D:Y.12, D:N.14, D:D.16, D:R.228

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Delatorre, P. et al., Crystal structure of Canavalia maritima seeds lectin (ConM) co-crystalized with gamma-aminobutyric acid (GABA) and soaked with adenine. To be Published

Release Date

2012-12-12

Peptides

Concanavalin-A: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Concanavalin-A

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