SMTL ID : 7s6r.1

Complex structure of Methane monooxygenase hydroxylase and regulatory subunit with H5A mutation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

hetero-2-2-2-2-mer

Ligands

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

FE.1: 6 residues within 4Å: Chain A: E.103, E.133, H.136, E.232 Ligands: FE.2, BEZ.7 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.103, A:E.133, A:H.136, H2O.1, H2O.2 FE.2: 6 residues within 4Å: Chain A: E.133, E.198, E.232, H.235 Ligands: FE.1, BEZ.7 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.133, A:E.198, A:E.232, A:H.235, H2O.1 FE.24: 6 residues within 4Å: Chain E: E.103, E.133, H.136, E.232 Ligands: FE.25, BEZ.29 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.103, E:E.133, E:H.136, H2O.48, H2O.50 FE.25: 6 residues within 4Å: Chain E: E.133, E.198, E.232, H.235 Ligands: FE.24, BEZ.29 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.133, E:E.198, E:E.232, E:H.235, H2O.50

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

EDO.3: 3 residues within 4Å: Chain A: W.330 Chain D: A.20, F.24 Ligand excluded by PLIP EDO.4: 2 residues within 4Å: Chain A: Q.395, A.399 Ligand excluded by PLIP EDO.5: 10 residues within 4Å: Chain A: R.87, E.90, T.91, V.94, Y.277, L.278, G.282, A.348, L.350 Ligands: EDO.9 Ligand excluded by PLIP EDO.6: 2 residues within 4Å: Chain A: D.510, K.514 Ligand excluded by PLIP EDO.8: 8 residues within 4Å: Chain A: R.175, G.180, N.192, N.262, A.263, T.266 Chain B: Q.74 Ligands: EDO.11 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: Y.277, A.339, W.343, L.350 Ligands: EDO.5 Ligand excluded by PLIP EDO.10: 2 residues within 4Å: Chain A: R.322, D.323 Ligand excluded by PLIP EDO.11: 7 residues within 4Å: Chain A: N.262, Q.445, E.449, R.452, Y.453 Chain C: Y.147 Ligands: EDO.8 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: R.66 Chain E: E.65, F.68, L.72 Ligands: EDO.23 Ligand excluded by PLIP EDO.13: 2 residues within 4Å: Chain B: S.307, E.308 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: F.68, L.72 Chain B: E.48, W.105, H.107 Chain H: K.96 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain B: Q.289, T.290 Chain E: P.9 Chain F: A.125 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain B: H.107, P.108, K.111 Ligand excluded by PLIP EDO.17: 3 residues within 4Å: Chain B: P.41, R.42, Y.301 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain B: Y.139, A.340, K.341, V.342 Ligand excluded by PLIP EDO.19: 7 residues within 4Å: Chain C: R.3, I.11, D.48, I.49, D.50, V.51, D.52 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain C: D.26, L.72, T.82, T.83, G.84 Ligand excluded by PLIP EDO.21: 7 residues within 4Å: Chain A: R.66 Chain D: E.46, K.96, F.98, D.102, I.105, N.106 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain B: R.9 Chain D: K.43, A.72 Chain E: R.77, L.78, G.79 Ligand excluded by PLIP EDO.23: 7 residues within 4Å: Chain D: K.96 Chain E: F.68, L.72, F.142 Chain F: E.48, H.107 Ligands: EDO.12 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain E: R.162, V.477, R.478, S.479, G.481 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain B: D.364 Chain E: L.3, K.4, V.5, R.7 Chain F: R.134 Ligand excluded by PLIP EDO.28: 3 residues within 4Å: Chain E: L.398, D.403, P.509 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain E: L.169, A.339, M.342, W.343, G.346 Ligand excluded by PLIP EDO.31: 5 residues within 4Å: Chain E: K.284, F.285, K.286, E.356, D.357 Ligand excluded by PLIP EDO.32: 2 residues within 4Å: Chain E: K.374, I.375 Ligand excluded by PLIP EDO.33: 6 residues within 4Å: Chain B: F.123, Y.127, T.275 Chain F: Q.266, P.278, A.282 Ligand excluded by PLIP EDO.34: 6 residues within 4Å: Chain A: P.9 Chain B: A.125, A.126 Chain F: T.286, Q.289, T.290 Ligand excluded by PLIP EDO.35: 6 residues within 4Å: Chain E: R.491, G.492 Chain F: A.22, A.23, V.24, P.25 Ligand excluded by PLIP EDO.36: 5 residues within 4Å: Chain F: Y.139, A.340, K.341, V.342, E.343 Ligand excluded by PLIP EDO.37: 4 residues within 4Å: Chain F: A.229, T.230, E.233, S.327 Ligand excluded by PLIP EDO.38: 6 residues within 4Å: Chain F: V.238, E.243, W.320, H.323, Y.324 Chain G: I.78 Ligand excluded by PLIP EDO.39: 7 residues within 4Å: Chain G: R.3, I.11, D.48, I.49, D.50, V.51, D.52 Ligand excluded by PLIP EDO.40: 4 residues within 4Å: Chain G: D.26, L.72, T.82, G.84 Ligand excluded by PLIP EDO.41: 4 residues within 4Å: Chain A: R.77 Chain F: R.9 Chain H: K.43, A.72 Ligand excluded by PLIP

2 x BEZ: BENZOIC ACID(Non-covalent)

BEZ.7: 14 residues within 4Å: Chain A: L.99, E.103, A.106, E.133, F.177, F.181, L.193, G.197, E.198, T.202, L.205, E.232 Ligands: FE.1, FE.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.99, A:F.177, A:F.177, A:F.181, A:L.193, A:E.198, A:T.202, A:L.205 BEZ.29: 14 residues within 4Å: Chain E: L.99, E.103, A.106, E.133, F.177, F.181, L.193, G.197, E.198, T.202, L.205, E.232 Ligands: FE.24, FE.25 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:L.99, E:F.177, E:F.177, E:F.181, E:E.198, E:T.202, E:L.205

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jones, J.C. et al., X-ray Crystal Structures of Methane Monooxygenase Hydroxylase Complexes with Variants of Its Regulatory Component: Correlations with Altered Reaction Cycle Dynamics. Biochemistry (2022)

Release Date

2021-12-29

Peptides

Methane monooxygenase component A alpha chain: AE
Methane monooxygenase beta chain: BF
Methane monooxygenase gamma chain: CG
Methane monooxygenase regulatory protein B: DH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

B
B

F
F

C
C

G
G

D
D

H
H

Methane monooxygenase component A alpha chain

Methane monooxygenase beta chain

Methane monooxygenase gamma chain

Methane monooxygenase regulatory protein B

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