SMTL ID : 3ujo.1

Galactose-specific seed lectin from Dolichos lablab in complex with adenine and galactose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x ADE: ADENINE(Non-covalent)

ADE.1: 9 residues within 4Å: Chain A: L.188, I.189, T.190, V.199, S.201, I.212, L.267 Chain C: S.201 Ligands: ADE.12 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:S.201, A:L.188 Water bridges: C:L.188, C:S.201 ADE.6: 8 residues within 4Å: Chain B: L.188, T.190, V.199, S.201, I.212 Chain D: S.201, V.203 Ligands: ADE.18 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:L.188, B:T.190, B:T.190, B:S.201, D:S.201 ADE.12: 9 residues within 4Å: Chain A: L.188, S.201 Chain C: L.188, I.189, T.190, V.199, S.201, I.212 Ligands: ADE.1 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:T.190, C:T.190, C:T.190, A:S.201, A:S.201 ADE.18: 10 residues within 4Å: Chain B: S.201, V.203 Chain D: L.188, I.189, T.190, V.199, S.201, I.212, L.267 Ligands: ADE.6 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:S.201, B:S.201, D:L.188

4 x GAL: beta-D-galactopyranose(Non-covalent)

GAL.2: 7 residues within 4Å: Chain A: G.125, G.126, F.150, N.152, G.236, L.237, Y.241 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.108, A:N.152, A:L.237 GAL.7: 10 residues within 4Å: Chain B: D.108, G.125, G.126, F.150, N.152, G.236, L.237, S.238, Y.241 Ligands: PEG.11 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.108, B:G.126, B:N.152, B:N.152, B:L.237, B:S.238 GAL.13: 10 residues within 4Å: Chain C: A.107, D.108, G.125, G.126, F.150, N.152, G.236, L.237, S.238, Y.241 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:D.108, C:G.126, C:N.152, C:N.152, C:L.237, C:S.238 GAL.19: 10 residues within 4Å: Chain D: A.107, D.108, G.125, G.126, F.150, N.152, G.236, L.237, S.238, Y.241 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.108, D:N.152, D:L.237

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

MN.3: 4 residues within 4Å: Chain A: E.146, D.148, D.156, H.161 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.148, A:D.156, A:H.161, H2O.1, H2O.1 MN.8: 4 residues within 4Å: Chain B: E.146, D.148, D.156, H.161 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.146, B:D.148, B:D.156, B:H.161, H2O.2, H2O.2 MN.14: 4 residues within 4Å: Chain C: E.146, D.148, D.156, H.161 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.146, C:D.148, C:D.156, C:H.161, H2O.3, H2O.3 MN.20: 4 residues within 4Å: Chain D: E.146, D.148, D.156, H.161 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.146, D:D.148, D:D.156, D:H.161

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 4 residues within 4Å: Chain A: D.148, F.150, N.152, D.156 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.148 CA.9: 4 residues within 4Å: Chain B: D.148, F.150, N.152, D.156 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.148, B:F.150, B:D.156, H2O.2, H2O.2 CA.15: 4 residues within 4Å: Chain C: D.148, F.150, N.152, D.156 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.148, C:F.150, C:D.156, H2O.3, H2O.4 CA.21: 4 residues within 4Å: Chain D: D.148, F.150, N.152, D.156 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.148, D:D.148, D:F.150, D:D.156

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 7 residues within 4Å: Chain A: S.28, F.29, T.30 Chain B: L.26, I.27, S.28 Chain C: K.266 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.28, A:F.29 EDO.10: 2 residues within 4Å: Chain B: S.49, K.51 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.49, B:K.51 EDO.16: 5 residues within 4Å: Chain C: A.65, G.66, L.237, S.238, K.239 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:L.237 EDO.22: 4 residues within 4Å: Chain D: S.194, T.195, N.196, R.216 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.195, D:N.196, D:R.216 EDO.23: 5 residues within 4Å: Chain D: N.97, G.182, E.183, N.184, S.206 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.97, D:G.182, D:N.184 Water bridges: D:E.183

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.11: 2 residues within 4Å: Chain B: L.237 Ligands: GAL.7 No protein-ligand interaction detected (PLIP) PEG.17: 2 residues within 4Å: Chain C: K.122, D.123 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.124

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shetty, K.N. et al., Affinity of a galactose-specific legume lectin from Dolichos lablab to adenine revealed by X-ray cystallography. Iubmb Life (2013)

Release Date

2012-11-14

Peptides

Legume lectin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Legume lectin

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