- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.30 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x MN: MANGANESE (II) ION(Non-covalent)
- 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 PLIPCL.9: 3 residues within 4Å:- Chain B: Y.12, Y.100
- Ligands: XMM.8
Ligand excluded by PLIPCL.14: 3 residues within 4Å:- Chain C: Y.12, Y.100
- Ligands: XMM.13
Ligand excluded by PLIPCL.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
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- 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
AB
AC
AD
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.30 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x MN: MANGANESE (II) ION(Non-covalent)
- 4 x CA: CALCIUM ION(Non-covalent)
- 4 x XMM: 5-bromo-4-chloro-1H-indol-3-yl alpha-D-mannopyranoside(Non-covalent)
- 4 x CL: CHLORIDE ION(Non-functional Binders)
- 4 x A3B: D-VINYLGLYCINE(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- 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
AB
AC
AD
A