SMTL ID : 1rit.1

Crystal structure of Peanut lectin in complex with meso-tetrasulphonatophenylporphyrin and lactose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

homo-tetramer

Ligands

2 x BGC- GAL: beta-D-galactopyranose-(1-4)-beta-D-glucopyranose(Non-covalent)

BGC-GAL.1: 12 residues within 4Å: Chain C: D.80, A.82, D.83, G.103, G.104, Y.125, N.127, E.129, S.211, L.212, G.213, G.214 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:S.211, C:L.212, C:G.213, C:D.80, C:D.83, C:G.104, C:N.127, C:S.211, C:S.211 Water bridges: C:G.102 BGC-GAL.2: 10 residues within 4Å: Chain D: D.80, D.83, G.103, G.104, Y.125, N.127, S.211, L.212, G.213, G.214 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.211, D:L.212, D:G.213, D:G.214, D:D.80, D:D.80, D:D.83, D:G.104, D:N.127, D:S.211

11 x SFP: 5,10,15,20-TETRAKIS(4-SULPFONATOPHENYL)-21H,23H-PORPHINE(Non-covalent)

SFP.3: 17 residues within 4Å: Chain A: T.25, L.27, N.29, N.31, Q.33, L.37, N.38, E.72, K.74, D.75, I.76, Y.79, I.217, L.219, R.221 Ligands: SFP.4, SFP.7 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:T.25, A:L.27, A:K.74, A:I.76, A:L.219 Hydrogen bonds: A:T.25, A:T.25, A:N.29, A:N.38, A:E.72, A:Y.79, A:R.221 pi-Cation interactions: A:K.74 SFP.4: 3 residues within 4Å: Chain A: S.28, N.29 Ligands: SFP.3 No protein-ligand interaction detected (PLIP) SFP.7: 5 residues within 4Å: Chain A: N.38, Y.79, R.215 Ligands: SFP.3, SFP.8 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.215 SFP.8: 7 residues within 4Å: Chain A: V.40, N.41, G.99, S.100, I.101, L.212 Ligands: SFP.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.40, A:V.40, A:I.101, A:L.212 Hydrogen bonds: A:N.41 SFP.9: 5 residues within 4Å: Chain B: N.38, Y.79, R.215 Ligands: SFP.10, SFP.11 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.215 SFP.10: 7 residues within 4Å: Chain B: V.40, N.41, G.99, S.100, I.101, L.212 Ligands: SFP.9 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.40, B:I.101, B:L.212 Hydrogen bonds: B:N.41 SFP.11: 14 residues within 4Å: Chain B: T.25, N.29, N.31, Q.33, L.37, N.38, E.72, D.75, I.76, Y.79, I.217, L.219, R.221 Ligands: SFP.9 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.217, B:L.219 Hydrogen bonds: B:N.29, B:N.29, B:N.38, B:R.221 pi-Cation interactions: B:K.74 SFP.14: 6 residues within 4Å: Chain C: R.53, S.56, A.58, T.59, T.231 Ligands: SFP.15 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:A.58, C:T.59 Hydrogen bonds: C:S.56, C:S.56, C:S.56 Salt bridges: C:R.53 SFP.15: 4 residues within 4Å: Chain C: R.53, A.58, R.201 Ligands: SFP.14 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:A.58 Hydrogen bonds: C:R.201 Salt bridges: C:R.53 SFP.18: 5 residues within 4Å: Chain D: R.53, S.56, T.59, T.231 Ligands: SFP.19 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:T.59 Hydrogen bonds: D:S.56, D:S.56, D:S.56 Salt bridges: D:R.53 SFP.19: 6 residues within 4Å: Chain D: R.53, S.57, A.58, E.200, R.201 Ligands: SFP.18 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:A.58 Hydrogen bonds: D:E.200, D:E.200 Salt bridges: D:R.53, D:R.201

4 x CA: CALCIUM ION(Non-covalent)

CA.5: 4 residues within 4Å: Chain A: D.123, Y.125, N.127, D.132 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.123, A:Y.125, A:D.132 CA.12: 5 residues within 4Å: Chain B: D.83, D.123, Y.125, N.127, D.132 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.123, B:D.123, B:Y.125 CA.16: 4 residues within 4Å: Chain C: D.123, Y.125, N.127, D.132 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.123, C:Y.125 CA.20: 4 residues within 4Å: Chain D: D.123, Y.125, N.127, D.132 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.123, D:D.123, D:Y.125, D:D.132

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

MN.6: 5 residues within 4Å: Chain A: E.121, D.123, D.132, H.137, V.145 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.121, A:D.123, A:H.137 MN.13: 5 residues within 4Å: Chain B: E.121, D.123, D.132, H.137, V.145 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.121, B:D.123, B:H.137 MN.17: 5 residues within 4Å: Chain C: E.121, D.123, D.132, H.137, S.147 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.121, C:D.123, C:D.132, C:H.137, H2O.1 MN.21: 6 residues within 4Å: Chain D: E.121, D.123, D.132, H.137, V.145, S.147 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.121, D:D.123, D:D.132, D:H.137

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Goel, M. et al., Crystal structures of the PNA-porphyrin complex in the presence and absence of lactose: mapping the conformational changes on lactose binding, interacting surfaces, and supramolecular aggregations. Biochemistry (2005)

Release Date

2004-12-28

Peptides

Galactose-binding lectin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Galactose-binding lectin

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