SMTL ID : 6ely.1

Crystal Structure of Mistletoe Lectin I (ML-I) from Viscum album in Complex with 4-N-Furfurylcytosine at 2.84 A Resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.84 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain B: Q.92, W.94, N.96, Y.126, L.228 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- GLA: alpha-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-GLA.2: 8 residues within 4Å: Chain A: F.214, N.215, P.217 Chain B: T.11, V.12, N.44, L.49, N.136 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.49 Hydrogen bonds: B:N.44

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 7 residues within 4Å: Chain A: Y.76, K.90, D.91, N.112, S.114, D.117, R.120 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.90, A:D.91, A:R.120 Water bridges: A:Y.76, A:D.91, A:N.112 NAG.20: 4 residues within 4Å: Chain B: D.27, F.29, N.61 Ligands: GOL.36 No protein-ligand interaction detected (PLIP)

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

CL.4: 3 residues within 4Å: Chain A: S.209, D.211 Chain B: S.6 Ligand excluded by PLIP CL.5: 1 residues within 4Å: Chain A: R.150 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: P.171, R.175, D.189, M.192 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain A: V.9 Ligand excluded by PLIP CL.8: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.21: 1 residues within 4Å: Chain B: G.158 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain B: Y.177, Q.188 Ligand excluded by PLIP CL.23: 1 residues within 4Å: Chain B: E.170 Ligand excluded by PLIP

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

SO4.9: 3 residues within 4Å: Chain A: S.65, G.83, R.143 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.65, A:G.83 Salt bridges: A:R.143 SO4.10: 6 residues within 4Å: Chain A: P.93, A.94, G.95, A.96, E.97, T.98 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.95, A:E.97, A:T.98 SO4.11: 6 residues within 4Å: Chain A: Y.115, E.119, H.124, R.125, D.126 Ligands: GOL.17 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.115, A:Y.115, A:R.125, A:D.126, A:D.126 Water bridges: A:D.126 Salt bridges: A:H.124, A:R.125 SO4.12: 5 residues within 4Å: Chain A: T.204, Q.205, H.208, N.215, N.216 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.205, A:N.215, A:N.216, A:N.216 Salt bridges: A:H.208 SO4.13: 3 residues within 4Å: Chain A: S.30, R.41, Q.42 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.42, A:Q.42 Salt bridges: A:R.41

17 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 2 residues within 4Å: Chain A: Q.134, S.185 Ligand excluded by PLIP GOL.15: 3 residues within 4Å: Chain A: S.148, T.149, R.150 Ligand excluded by PLIP GOL.16: 7 residues within 4Å: Chain A: Q.134, Q.137, S.138, A.141, R.154, S.155, I.158 Ligand excluded by PLIP GOL.17: 4 residues within 4Å: Chain A: Y.115, E.119, H.124 Ligands: SO4.11 Ligand excluded by PLIP GOL.24: 7 residues within 4Å: Chain A: R.234, D.235 Chain B: L.133, R.141, L.176, Y.177, G.178 Ligand excluded by PLIP GOL.25: 5 residues within 4Å: Chain A: W.174, R.175, Q.178 Chain B: Y.146, D.150 Ligand excluded by PLIP GOL.26: 4 residues within 4Å: Chain B: T.51, K.53, R.59, G.62 Ligand excluded by PLIP GOL.27: 3 residues within 4Å: Chain B: F.29, Q.30, D.31 Ligand excluded by PLIP GOL.28: 8 residues within 4Å: Chain B: D.23, V.24, R.25, D.26, Q.36, W.38, K.41, N.47 Ligand excluded by PLIP GOL.29: 3 residues within 4Å: Chain B: Q.190, V.206, S.207 Ligand excluded by PLIP GOL.30: 4 residues within 4Å: Chain B: E.142, E.170, R.173, K.185 Ligand excluded by PLIP GOL.31: 5 residues within 4Å: Chain B: D.28, Q.30, D.31, G.32, N.33 Ligand excluded by PLIP GOL.32: 3 residues within 4Å: Chain B: A.72, Q.122, T.123 Ligand excluded by PLIP GOL.33: 7 residues within 4Å: Chain A: V.228, T.229, L.230, D.235 Chain B: R.141, V.143, P.263 Ligand excluded by PLIP GOL.34: 4 residues within 4Å: Chain B: D.235, Q.238, Y.249, N.256 Ligand excluded by PLIP GOL.35: 2 residues within 4Å: Chain B: D.80, N.82 Ligand excluded by PLIP GOL.36: 1 residues within 4Å: Ligands: NAG.20 Ligand excluded by PLIP

2 x GLY: GLYCINE(Non-covalent)

GLY.18: 8 residues within 4Å: Chain A: W.174, R.177 Chain B: G.147, F.148, R.149, D.150, P.255, M.258 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.177, A:R.177, B:R.149, B:D.150 Salt bridges: A:R.177 GLY.37: 2 residues within 4Å: Chain B: K.53, R.59 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.53, B:K.53 Salt bridges: B:R.59

1 x BFW: 4-N-Furfurylcytosine(Non-covalent)

BFW.19: 10 residues within 4Å: Chain A: Y.76, G.113, S.114, Y.115, E.119, R.125, L.157, E.165, R.168, E.196 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.157 Hydrogen bonds: A:E.165, A:E.165, A:R.168, A:R.168 Water bridges: A:Y.76

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ahmad, M.S. et al., Crystal Structure of Mistletoe Lectin I (ML-I) from Viscum album in Complex with 4-N-Furfurylcytosine at 2.85 angstrom Resolution. Med Chem (2018)

Release Date

2018-05-02

Peptides

Mistletoe Lectin I: A
Mistletoe Lectin I: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Mistletoe Lectin I

Mistletoe Lectin I