SMTL ID : 6trv.1

Structure of SapL1 lectin in complex with alpha methyl fucoside

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

9 x MFU: methyl alpha-L-fucopyranoside(Non-covalent)

MFU.1: 7 residues within 4Å: Chain A: R.25, E.37, F.69, I.72, W.88, W.93 Ligands: GOL.6 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.69, A:I.72 Hydrogen bonds: A:R.25, A:E.37 Water bridges: A:E.37, A:E.37 Salt bridges: A:R.25 MFU.2: 9 residues within 4Å: Chain A: R.73, E.85, Y.94, G.96, A.97, F.98, I.117, W.135, W.142 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.117 Hydrogen bonds: A:E.85, A:A.97, A:F.98 Salt bridges: A:R.73 MFU.3: 10 residues within 4Å: Chain A: R.170, E.182, Y.191, G.193, G.194, L.195, L.218, I.220, W.236, W.242 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.218, A:I.220, A:W.236 Hydrogen bonds: A:Y.172, A:E.182, A:G.194, A:L.195 Salt bridges: A:R.170 MFU.4: 9 residues within 4Å: Chain A: R.221, E.233, Y.243, G.245, G.246, F.247, L.265, W.283, W.287 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.265, A:W.283 Hydrogen bonds: A:E.233, A:G.246, A:F.247 Water bridges: A:D.244 Salt bridges: A:R.221 MFU.5: 9 residues within 4Å: Chain A: S.22, L.24, Y.40, W.44, V.264, R.266, E.280, G.290, Q.291 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.40, A:V.264 Hydrogen bonds: A:R.266, A:E.280, A:G.290 Salt bridges: A:R.266 MFU.11: 10 residues within 4Å: Chain B: R.73, E.85, C.87, Y.94, G.96, A.97, F.98, I.117, W.135, W.142 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.117 Hydrogen bonds: B:R.73, B:E.85, B:A.97, B:F.98 Salt bridges: B:R.73 MFU.12: 10 residues within 4Å: Chain B: R.170, E.182, Y.191, G.193, G.194, L.195, L.218, I.220, W.236, W.242 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.218, B:I.220, B:W.236 Hydrogen bonds: B:E.182, B:Y.191, B:G.194, B:L.195 Salt bridges: B:R.170 MFU.13: 9 residues within 4Å: Chain B: R.221, E.233, Y.243, G.245, G.246, F.247, L.265, W.283, W.287 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.265 Hydrogen bonds: B:R.221, B:E.233, B:Y.243, B:G.246, B:F.247 Salt bridges: B:R.221 MFU.14: 7 residues within 4Å: Chain B: S.22, L.24, Y.40, W.44, R.266, E.280, G.290 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.24, B:Y.40 Hydrogen bonds: B:R.266, B:E.280, B:G.290 Salt bridges: B:R.266

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: R.25, E.37, W.88, W.93 Ligands: MFU.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.25, A:Y.27 Water bridges: A:E.37, A:E.37 GOL.7: 5 residues within 4Å: Chain A: R.120, E.132, I.169, W.185, W.190 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.120, A:A.146 GOL.8: 6 residues within 4Å: Chain A: I.18, R.19, T.65, S.66, I.260, P.261 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.19, A:T.65, A:S.66, A:S.66 GOL.9: 7 residues within 4Å: Chain A: A.16, A.17, A.63, A.64, A.208, A.258, A.259 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:A.17, A:A.64, A:A.64, A:A.208, A:A.208, A:A.259 Water bridges: A:A.159 GOL.15: 5 residues within 4Å: Chain B: R.25, E.37, I.72, W.88, W.93 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.37 GOL.16: 6 residues within 4Å: Chain B: R.120, E.132, A.146, I.169, W.185, W.190 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.120 Water bridges: B:W.190 GOL.17: 7 residues within 4Å: Chain B: A.159, T.160, S.161, A.208, T.209, S.210, P.261 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.161, B:A.208, B:T.209

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.10: 2 residues within 4Å: Chain A: R.19, P.263 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.19, A:N.21 Salt bridges: A:R.19

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Martinez-Alarcon, D. et al., Biochemical and structural studies of target lectin SapL1 from the emerging opportunistic microfungus Scedosporium apiospermum. Sci Rep (2021)

Release Date

2020-12-23

Peptides

Uncharacterized protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

Uncharacterized protein