SMTL ID : 6vk6.1

Crystal Structure of Methylosinus trichosporium OB3b Soluble Methane Monooxygenase Hydroxylase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 x FE: FE (III) ION(Non-covalent)

FE.1: 7 residues within 4Å: Chain A: E.114, E.144, H.147, E.243, H.246 Ligands: FE.2, EDO.12 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.114, A:E.144, A:H.147, H2O.2, H2O.3 FE.2: 7 residues within 4Å: Chain A: Q.140, E.144, E.209, E.243, H.246 Ligands: FE.1, EDO.12 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.144, A:E.209, A:E.243, A:H.246, H2O.3

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

EDO.3: 6 residues within 4Å: Chain A: K.295, F.296, K.297, E.367, D.368, W.371 Ligand excluded by PLIP EDO.4: 9 residues within 4Å: Chain A: V.62, I.63, A.64, Y.67, N.135, G.136, L.138, A.139 Chain B: L.187 Ligand excluded by PLIP EDO.5: 9 residues within 4Å: Chain A: A.210, C.211, N.214, P.215, M.247, W.308, D.312, W.313, W.317 Ligand excluded by PLIP EDO.6: 8 residues within 4Å: Chain A: V.105, F.109, L.180, G.357, F.358, A.359 Ligands: EDO.7, EDO.25 Ligand excluded by PLIP EDO.7: 10 residues within 4Å: Chain A: R.98, E.101, T.102, V.105, Y.288, L.289, G.293, A.359, L.361 Ligands: EDO.6 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: V.302, Y.340, W.341, Y.376, P.377 Ligand excluded by PLIP EDO.9: 7 residues within 4Å: Chain A: W.276, D.334, T.433, R.437, D.450, D.451, W.452 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: H.382, S.428, L.429, A.430, K.431 Ligands: EDO.19 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: L.14, K.15, V.16, R.18 Chain B: R.137 Ligands: EDO.17 Ligand excluded by PLIP EDO.12: 15 residues within 4Å: Chain A: G.113, E.114, A.117, Q.140, E.144, H.147, F.188, F.192, L.204, E.209, T.213, E.243, H.246 Ligands: FE.1, FE.2 Ligand excluded by PLIP EDO.13: 7 residues within 4Å: Chain A: D.12, K.15, V.16, N.17 Chain B: L.206, V.207, P.208 Ligand excluded by PLIP EDO.14: 7 residues within 4Å: Chain A: K.49, D.260, P.261, A.262, K.265, F.266 Chain C: E.142 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain A: L.409, A.410, N.411, G.412 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain A: A.73, K.74, R.77 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain A: L.14, K.15 Chain B: R.137 Ligands: EDO.11 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain A: K.385, I.386, E.389, W.407 Ligands: EDO.19 Ligand excluded by PLIP EDO.19: 8 residues within 4Å: Chain A: D.381, H.382, K.385, I.386, W.407, L.429 Ligands: EDO.10, EDO.18 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain A: A.258, A.264, K.323, Y.324, G.325 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain A: L.237, S.238, T.241 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain A: P.20, V.21, G.22, V.23, E.24 Chain B: K.205 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain A: K.297, V.298, E.299, P.300, W.371 Ligand excluded by PLIP EDO.24: 6 residues within 4Å: Chain A: E.477, S.479, E.480, A.483, L.509, K.513 Ligand excluded by PLIP EDO.25: 12 residues within 4Å: Chain A: G.178, P.179, L.180, Y.288, A.349, A.350, M.353, W.354, L.356, G.357, L.361 Ligands: EDO.6 Ligand excluded by PLIP EDO.28: 6 residues within 4Å: Chain A: F.79, L.83, F.153 Chain B: E.51, W.108, H.110 Ligand excluded by PLIP EDO.29: 8 residues within 4Å: Chain B: D.145, E.146, N.149, K.150, G.209, F.210, D.211 Ligands: CL.26 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain B: F.126, Y.130, T.278, P.281, F.282 Ligand excluded by PLIP EDO.31: 5 residues within 4Å: Chain B: Y.142, A.343, K.344, V.345, E.346 Ligand excluded by PLIP EDO.32: 4 residues within 4Å: Chain A: K.160 Chain B: R.36, K.37, Q.54 Ligand excluded by PLIP EDO.33: 7 residues within 4Å: Chain B: G.229, A.232, T.233, E.236, H.326, Y.327, S.330 Ligand excluded by PLIP EDO.34: 7 residues within 4Å: Chain A: T.501, R.502, G.503 Chain B: A.25, A.26, V.27, P.28 Ligand excluded by PLIP EDO.35: 7 residues within 4Å: Chain B: N.308, D.309, S.310, E.311, F.312, G.313, A.314 Ligand excluded by PLIP EDO.36: 6 residues within 4Å: Chain B: E.311, F.312 Chain C: E.63, K.64, V.67 Ligands: EDO.47 Ligand excluded by PLIP EDO.37: 9 residues within 4Å: Chain B: Y.342, A.343, V.345, E.346, K.347, V.348, T.352, D.353, Y.393 Ligand excluded by PLIP EDO.38: 2 residues within 4Å: Chain B: Q.292, T.293 Ligand excluded by PLIP EDO.39: 8 residues within 4Å: Chain B: D.64, I.66, A.67, G.68, G.69, L.70 Chain C: Y.56, R.59 Ligand excluded by PLIP EDO.42: 8 residues within 4Å: Chain C: R.4, I.12, Y.48, D.49, I.50, D.51, V.52, D.53 Ligand excluded by PLIP EDO.43: 6 residues within 4Å: Chain C: V.26, D.27, L.73, T.83, T.84, G.85 Ligand excluded by PLIP EDO.44: 8 residues within 4Å: Chain A: S.435, R.437, D.451, E.454 Chain C: L.153, R.157, L.167, Q.168 Ligand excluded by PLIP EDO.45: 3 residues within 4Å: Chain C: A.93, T.94, A.97 Ligand excluded by PLIP EDO.46: 5 residues within 4Å: Chain C: K.31, Q.34, D.35, L.38, L.118 Ligand excluded by PLIP EDO.47: 6 residues within 4Å: Chain C: K.64, V.67, L.68, E.71, K.72 Ligands: EDO.36 Ligand excluded by PLIP EDO.48: 6 residues within 4Å: Chain A: Y.416, P.427, L.436, F.526 Chain C: H.166, Q.168 Ligand excluded by PLIP

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

CL.26: 7 residues within 4Å: Chain B: R.144, D.145, V.207, P.208, G.209, F.210 Ligands: EDO.29 Ligand excluded by PLIP CL.27: 3 residues within 4Å: Chain B: F.41, Y.58, L.70 Ligand excluded by PLIP CL.40: 4 residues within 4Å: Chain C: A.39, Y.40, K.46, S.47 Ligand excluded by PLIP CL.41: 1 residues within 4Å: Chain C: E.86 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jones, J.C. et al., Structural Studies of theMethylosinus trichosporiumOB3b Soluble Methane Monooxygenase Hydroxylase and Regulatory Component Complex Reveal a Transient Substrate Tunnel. Biochemistry (2020)

Release Date

2020-08-05

Peptides

Methane monooxygenase component A alpha chain: A
Methane monooxygenase: B
Methane monooxygenase: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Methane monooxygenase component A alpha chain

Methane monooxygenase

Methane monooxygenase

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