SMTL ID : 7ron.1

Crystal structure of the Friedel-Crafts alkylating enzyme CylK from Cylindospermum licheniforme

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

monomer

Ligands

9 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 6 residues within 4Å: Chain A: N.367, E.373, Y.417, A.419, Q.427 Ligands: EDO.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.367, A:E.373, A:Q.427 Water bridges: A:Y.417 EDO.2: 6 residues within 4Å: Chain A: A.350, K.365, Q.366, N.367, F.421 Ligands: EDO.1 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.388, A:Y.417 EDO.3: 3 residues within 4Å: Chain A: V.430, A.431, Q.432 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.432, A:Q.432 EDO.4: 3 residues within 4Å: Chain A: L.284, Q.305, S.308 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.305, A:S.308 Water bridges: A:Y.299, A:S.308 EDO.5: 4 residues within 4Å: Chain A: S.10, A.14, L.172, Y.218 No protein-ligand interaction detected (PLIP) EDO.6: 3 residues within 4Å: Chain A: R.306, W.307, R.309 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.309, A:R.309 Water bridges: A:S.308, A:S.308 EDO.7: 6 residues within 4Å: Chain A: S.108, D.109, S.110, S.152, R.154, Y.587 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.152, A:R.154 Water bridges: A:S.152, A:S.586 EDO.8: 3 residues within 4Å: Chain A: L.12, D.15, S.205 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.15, A:D.15 EDO.9: 5 residues within 4Å: Chain A: D.168, D.169, E.214, G.217, Y.218 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.168, A:D.168, A:D.169, A:Y.218 Water bridges: A:D.168, A:Y.218

11 x CA: CALCIUM ION(Non-covalent)

CA.10: 7 residues within 4Å: Chain A: T.84, S.86, D.88, G.104, R.105, H.106, D.109 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:T.84, A:S.86, A:G.104, A:H.106, A:D.109 CA.11: 7 residues within 4Å: Chain A: R.105, H.106, G.107, D.109, G.131, D.132, D.153 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:R.105, A:G.107, A:D.109, A:G.131, A:D.132, A:D.153 CA.12: 4 residues within 4Å: Chain A: D.132, W.151, D.153, D.188 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.132, A:W.151, A:D.153, A:D.188, H2O.4, H2O.11 CA.13: 6 residues within 4Å: Chain A: Y.165, E.167, G.173, Q.176, D.219, L.220 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:Y.165, A:E.167, A:G.173, A:Q.176, A:D.219, A:L.220 CA.14: 6 residues within 4Å: Chain A: T.257, A.259, D.261, G.641, Y.643, D.644 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:T.257, A:A.259, A:D.261, A:G.641, A:Y.643, A:D.644 CA.15: 6 residues within 4Å: Chain A: G.290, R.292, D.293, S.313, G.315, E.317 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:G.290, A:R.292, A:D.293, A:S.313, A:G.315, A:E.317 CA.16: 4 residues within 4Å: Chain A: N.348, D.349, T.369, T.371 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:N.348, A:D.349, A:T.369, A:T.371, H2O.5, H2O.8 CA.17: 6 residues within 4Å: Chain A: S.413, T.414, D.415, T.435, T.437, D.439 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:S.413, A:T.414, A:D.415, A:T.435, A:T.437, A:D.439 CA.18: 5 residues within 4Å: Chain A: Y.473, D.474, T.494, N.496, D.498 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:Y.473, A:D.474, A:T.494, A:N.496, A:D.498, H2O.9 CA.19: 6 residues within 4Å: Chain A: G.527, Y.529, D.530, T.550, E.552, D.554 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:G.527, A:Y.529, A:D.530, A:T.550, A:E.552, A:D.554 CA.20: 6 residues within 4Å: Chain A: G.585, Y.587, D.588, T.608, D.610, D.612 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:G.585, A:Y.587, A:D.588, A:T.608, A:D.610, A:D.612

2 x MG: MAGNESIUM ION(Non-covalent)

MG.21: 3 residues within 4Å: Chain A: D.502, D.559, I.561 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.502, A:D.559, A:I.561, H2O.3, H2O.7 MG.22: 2 residues within 4Å: Chain A: A.77, S.80 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:A.77, A:S.80, H2O.11, H2O.12, H2O.13

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

CL.23: 5 residues within 4Å: Chain A: T.84, V.85, R.105, Y.473, F.499 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Braffman, N.R. et al., Structural basis for an unprecedented enzymatic alkylation in cylindrocyclophane biosynthesis. Elife (2022)

Release Date

2022-03-23

Peptides

CylK: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

CylK

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