SMTL ID : 5ul3.1

Structure of Cobalamin-dependent S-adenosylmethionine radical enzyme OxsB with aqua-cobalamin bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.1: 9 residues within 4Å: Chain A: C.313, S.316, R.317, C.318, F.320, C.321, R.323, R.399 Ligands: DTT.3 4 PLIP interactions: 4 interactions with chain A, Salt bridges: A:E.363 Metal complexes: A:C.313, A:C.318, A:C.321

1 x B12: COBALAMIN(Non-covalent)

B12.2: 30 residues within 4Å: Chain A: F.131, R.135, L.138, S.139, T.142, L.143, Q.161, G.182, L.183, S.184, F.187, T.214, G.216, N.217, C.237, K.239, E.240, G.241, E.242, E.308, R.311, C.321, P.322, H.325, K.326, A.361, E.363, E.545 Ligands: DTT.3, EDO.21 32 PLIP interactions: 30 interactions with chain A, 2 Ligand-Water interactions Hydrophobic interactions: A:F.131, A:F.131, A:L.143, A:F.187, A:K.326, A:A.361, A:E.363 Hydrogen bonds: A:R.135, A:R.135, A:Q.161, A:F.187, A:N.217, A:N.217, A:G.241, A:E.242, A:E.308, A:P.322, A:H.325, A:E.363, A:E.363, A:E.363, A:E.545 Water bridges: A:N.137, A:N.137, A:S.139, A:S.139, A:Q.161, A:N.217, A:K.326 Salt bridges: A:K.326 Metal complexes: H2O.20, H2O.20

1 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.3: 6 residues within 4Å: Chain A: D.362, E.363, A.397 Ligands: SF4.1, B12.2, EDO.23 No protein-ligand interaction detected (PLIP)

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.4: 4 residues within 4Å: Chain A: R.317, E.368, L.369, P.370 5 PLIP interactions: 5 interactions with chain A Water bridges: A:D.314, A:Y.315, A:R.317 Salt bridges: A:R.317, A:E.368

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

EDO.5: 4 residues within 4Å: Chain A: I.467, N.468, L.469, L.499 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: L.469, R.470, I.536, V.537, R.634 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: M.475, L.493, Y.534, M.540, L.541, H.638 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: Y.539, M.540, I.601, H.633 Ligands: EDO.28 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: L.614, V.617, T.714, D.715 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: D.703, A.706, D.707, K.710 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: K.257, L.258, D.259, E.269 Ligand excluded by PLIP EDO.12: 2 residues within 4Å: Chain A: D.259, N.276 Ligand excluded by PLIP EDO.13: 2 residues within 4Å: Chain A: E.150, E.286 Ligand excluded by PLIP EDO.14: 3 residues within 4Å: Chain A: L.14, P.75, Y.101 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain A: T.373, Q.376, R.377, D.380 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain A: K.588, T.589, N.592, G.681 Ligand excluded by PLIP EDO.17: 1 residues within 4Å: Chain A: M.251 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain A: L.327, R.328, S.329 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain A: Y.627, M.630, E.631, R.634 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain A: Y.201, R.230, Y.231, P.232, S.233 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain A: R.135, Y.359 Ligands: B12.2 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain A: I.24, T.56, D.57, D.344, R.347 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain A: F.432, E.436, G.472, F.473, I.474 Ligands: DTT.3 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain A: F.320, I.474, S.543, M.544, E.545 Ligand excluded by PLIP EDO.25: 3 residues within 4Å: Chain A: E.94, I.95, E.96 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain A: S.221, F.222, D.238, K.239, D.324 Ligand excluded by PLIP EDO.27: 4 residues within 4Å: Chain A: H.665, K.699, L.700, D.703 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain A: S.538, Y.539, M.540, R.634 Ligands: EDO.8 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bridwell-Rabb, J. et al., A B12-dependent radical SAM enzyme involved in oxetanocin A biosynthesis. Nature (2017)

Release Date

2017-04-19

Peptides

OxsB protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

OxsB protein

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