SMTL ID : 3sh3.1

Crystal structure of a pro-inflammatory lectin from the seeds of Dioclea wilsonii STANDL

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: E.8, D.10, D.19, H.24 Ligands: CA.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.8, A:D.10, A:D.19, A:H.24, H2O.1 MN.6: 5 residues within 4Å: Chain B: E.8, D.10, D.19, H.24 Ligands: CA.7 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.8, B:D.10, B:D.19, B:H.24, H2O.4 MN.11: 5 residues within 4Å: Chain C: E.8, D.10, D.19, H.24 Ligands: CA.12 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.8, C:D.10, C:D.19, C:H.24, H2O.7 MN.16: 5 residues within 4Å: Chain D: E.8, D.10, D.19, H.24 Ligands: CA.17 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.8, D:D.10, D:D.19, D:H.24, H2O.10

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: D.10, Y.12, N.14, D.19 Ligands: MN.1 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.1 CA.7: 5 residues within 4Å: Chain B: D.10, Y.12, N.14, D.19 Ligands: MN.6 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.10, B:Y.12, B:D.19, H2O.4, H2O.4 CA.12: 5 residues within 4Å: Chain C: D.10, Y.12, N.14, D.19 Ligands: MN.11 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.10, C:Y.12, C:D.19, H2O.7, H2O.7 CA.17: 5 residues within 4Å: Chain D: D.10, Y.12, N.14, D.19 Ligands: MN.16 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.10, D:Y.12, D:D.19, H2O.10, H2O.10

4 x XMM: 5-bromo-4-chloro-1H-indol-3-yl alpha-D-mannopyranoside(Non-covalent)

XMM.3: 10 residues within 4Å: Chain A: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 Ligands: CL.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.99 Hydrogen bonds: A:Y.12, A:N.14, A:G.98, A:L.99, A:Y.100, A:Y.100, A:R.228 XMM.8: 10 residues within 4Å: Chain B: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 Ligands: CL.9 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.99 Hydrogen bonds: B:Y.12, B:N.14, B:G.98, B:L.99, B:Y.100, B:Y.100, B:R.228 XMM.13: 10 residues within 4Å: Chain C: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 Ligands: CL.14 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:L.99 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 XMM.18: 10 residues within 4Å: Chain D: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 Ligands: CL.19 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:L.99 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

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 3 residues within 4Å: Chain A: Y.12, Y.100 Ligands: XMM.3 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: Y.12, Y.100 Ligands: XMM.8 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain C: Y.12, Y.100 Ligands: XMM.13 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain D: Y.12, Y.100 Ligands: XMM.18 Ligand excluded by PLIP

4 x A3B: D-VINYLGLYCINE(Non-covalent)

A3B.5: 11 residues within 4Å: Chain A: S.113, K.114, L.115, N.124, S.125, L.126, P.178, V.179, H.180 Chain D: F.130, D.139 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:L.115, A:L.126, A:V.179 Hydrogen bonds: A:S.125, A:H.180, D:D.139, D:D.139 Water bridges: A:N.124, A:N.124 A3B.10: 11 residues within 4Å: Chain B: S.113, K.114, L.115, N.124, S.125, L.126, P.178, V.179, H.180 Chain C: F.130, D.139 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:L.115, B:L.126, B:V.179 Hydrogen bonds: B:S.125, B:H.180, C:D.139, C:D.139 Water bridges: B:N.124, B:N.124 A3B.15: 11 residues within 4Å: Chain B: F.130, D.139 Chain C: S.113, K.114, L.115, N.124, S.125, L.126, P.178, V.179, H.180 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:L.115, C:L.126, C:V.179 Hydrogen bonds: C:S.125, C:H.180, B:D.139 Water bridges: C:N.124, C:N.124 A3B.20: 11 residues within 4Å: Chain A: F.130, D.139 Chain D: S.113, K.114, L.115, N.124, S.125, L.126, P.178, V.179, H.180 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:L.115, D:L.126, D:V.179 Hydrogen bonds: D:S.125, D:H.180, A:D.139 Water bridges: D:N.124, D:N.124

Links

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Citation

Rangel, T.B. et al., Crystal structure of a pro-inflammatory lectin from the seeds of Dioclea wilsonii Standl. Biochimie (2012)

Release Date

2011-10-05

Peptides

Lectin alpha chain: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Lectin alpha chain