SMTL ID : 6b11.1 (1 other biounit)

TylHI in complex with native substrate 23-deoxy-5-O-mycaminosyl-tylonolide (23-DMTL)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

monomer

Ligands

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 29 residues within 4Å: Chain A: L.130, L.131, H.138, R.142, F.149, I.194, L.275, L.276, G.280, T.283, T.284, I.325, A.326, L.329, R.331, L.354, A.381, F.382, G.383, P.386, H.387, C.389, L.390, G.391, L.394, A.395, E.398 Ligands: CGM.2, EDO.12 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:L.131, A:L.131, A:F.149, A:I.194, A:L.275, A:L.276, A:T.283, A:I.325, A:A.326, A:L.354, A:F.382, A:L.390, A:L.394 Salt bridges: A:H.138, A:R.142, A:R.331, A:H.387 pi-Stacking: A:F.382 Metal complexes: A:C.389

1 x CGM: (4R,5S,6S,7R,9R,11E,13E,15S,16R)-16-ethyl-4-hydroxy-5,9,13,15-tetramethyl-2,10-dioxo-7-(2-oxoethyl)-1-oxacyclohexadeca-11,13-dien-6-yl 3,6-dideoxy-3-(dimethylamino)-beta-D-glucopyranoside(Non-covalent)

CGM.2: 22 residues within 4Å: Chain A: S.120, D.121, G.122, E.123, E.125, L.131, A.215, R.217, P.218, A.220, A.224, L.225, L.228, L.231, V.274, L.275, A.278, A.326, A.429 Ligands: HEM.1, EDO.12, EDO.13 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:E.125, A:L.131, A:P.218, A:L.231, A:V.274, A:L.275, A:A.278, A:A.326, A:A.429 Hydrogen bonds: A:G.122, A:E.123, A:A.215 Water bridges: A:R.116

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

EDO.3: 6 residues within 4Å: Chain A: F.63, V.294, Q.297, H.298, Y.322 Ligands: EDO.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.322, A:Y.322 EDO.4: 2 residues within 4Å: Chain A: D.96, R.99 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.99 Water bridges: A:Q.95 EDO.5: 3 residues within 4Å: Chain A: R.106, I.337, E.338 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.106, A:R.106, A:E.338 EDO.6: 6 residues within 4Å: Chain A: P.56, L.117, P.218, A.219, D.427, S.428 2 PLIP interactions: 2 interactions with chain A Water bridges: A:A.219, A:D.427 EDO.7: 1 residues within 4Å: Chain A: R.414 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.414 EDO.8: 2 residues within 4Å: Chain A: T.416, T.417 No protein-ligand interaction detected (PLIP) EDO.9: 5 residues within 4Å: Chain A: E.361, A.362, V.363, F.364, S.365 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.362 EDO.10: 4 residues within 4Å: Chain A: T.173, A.174, G.176 Ligands: EDO.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.173 EDO.11: 2 residues within 4Å: Chain A: D.177 Ligands: EDO.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.177 EDO.12: 7 residues within 4Å: Chain A: L.114, L.329, R.330, R.331 Ligands: HEM.1, CGM.2, EDO.13 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.330, A:R.330, A:R.331 Water bridges: A:L.131 EDO.13: 5 residues within 4Å: Chain A: G.328, L.329, R.330 Ligands: CGM.2, EDO.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.328, A:R.330, A:R.330 EDO.14: 2 residues within 4Å: Chain A: D.418, A.420 No protein-ligand interaction detected (PLIP) EDO.15: 7 residues within 4Å: Chain A: D.317, E.318, R.321, F.364, A.376, R.377, H.379 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.377 Water bridges: A:G.314, A:R.374 EDO.16: 6 residues within 4Å: Chain A: H.298, Y.322, E.368, A.369, F.370 Ligands: EDO.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.322

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

DeMars, M.D. et al., TylHI in complex with native substrate 23-deoxy-5-O-mycaminosyl-tylonolide (23-DMTL). To Be Published

Release Date

2018-12-19

Peptides

20-oxo-5-O-mycaminosyltylactone 23-monooxygenase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

20-oxo-5-O-mycaminosyltylactone 23-monooxygenase

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