SMTL ID : 7roo.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

monomer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: N.367, E.373, Y.417, Q.427, V.430 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: 7 residues within 4Å: Chain A: A.350, Y.351, 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: N.525, G.527, S.528 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.528 EDO.4: 2 residues within 4Å: Chain A: N.539, N.541 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.541 EDO.5: 6 residues within 4Å: Chain A: S.108, D.109, S.110, S.152, R.154, Y.587 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.152, A:R.154 Water bridges: A:S.152, A:R.154, A:S.586 EDO.6: 3 residues within 4Å: Chain A: L.284, Q.305, S.308 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.305, A:S.308 Water bridges: A:S.308 EDO.7: 7 residues within 4Å: Chain A: A.464, K.465, N.466, T.467, D.474, Q.491, G.493 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.467, A:T.467

4 x BR: BROMIDE ION(Non-covalent)

BR.8: 4 residues within 4Å: Chain A: T.84, R.105, Y.473, F.499 Ligand excluded by PLIP BR.9: 3 residues within 4Å: Chain A: E.136, Q.137, G.148 Ligand excluded by PLIP BR.10: 1 residues within 4Å: Chain A: P.48 Ligand excluded by PLIP BR.11: 3 residues within 4Å: Chain A: E.317, S.318, W.320 Ligand excluded by PLIP

10 x CA: CALCIUM ION(Non-covalent)

CA.12: 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.13: 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.14: 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.5, H2O.11 CA.15: 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.16: 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.17: 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.18: 6 residues within 4Å: Chain A: S.413, T.414, D.415, T.435, T.437, D.439 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:T.414, A:D.415, A:T.435, A:T.437, A:D.439 CA.19: 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.11 CA.20: 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.21: 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.22: 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.2, H2O.7 MG.23: 2 residues within 4Å: Chain A: G.285, S.308 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:G.285, A:S.308, A:S.308, H2O.11, H2O.14, H2O.14

1 x NA: SODIUM ION(Non-functional Binders)

NA.24: 2 residues within 4Å: Chain A: K.162, F.166 No protein-ligand interaction detected (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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