SMTL ID : 7ev9.1

cryoEM structure of particulate methane monooxygenase associated with Cu(I)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

24 x CU1: COPPER (I) ION(Non-covalent)

CU1.1: 3 residues within 4Å: Chain A: H.48, H.72, Q.404 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.48, A:H.72 CU1.2: 4 residues within 4Å: Chain A: H.33, H.137, H.139 Ligands: CU1.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.33 CU1.3: 4 residues within 4Å: Chain A: H.33, H.137, H.139 Ligands: CU1.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.137, A:H.139 CU1.4: 5 residues within 4Å: Chain A: E.316, R.323, Y.330, F.394, R.400 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.316 CU1.5: 3 residues within 4Å: Chain A: S.310, D.395 Ligands: CU1.6 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.395, A:D.395 CU1.6: 6 residues within 4Å: Chain A: T.281, V.282, N.306, G.308, I.312 Ligands: CU1.5 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.281 CU1.7: 6 residues within 4Å: Chain B: H.38, M.42, F.50, N.103, R.104 Chain C: E.125 No protein-ligand interaction detected (PLIP) CU1.8: 4 residues within 4Å: Chain B: H.38, A.41, M.42, E.100 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.100 CU1.9: 3 residues within 4Å: Chain D: H.48, H.72, Q.404 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:H.48, D:H.72 CU1.10: 4 residues within 4Å: Chain D: H.33, H.137, H.139 Ligands: CU1.11 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:H.33 CU1.11: 4 residues within 4Å: Chain D: H.33, H.137, H.139 Ligands: CU1.10 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:H.137, D:H.139 CU1.12: 5 residues within 4Å: Chain D: E.316, R.323, Y.330, F.394, R.400 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.316 CU1.13: 3 residues within 4Å: Chain D: S.310, D.395 Ligands: CU1.14 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.395, D:D.395 CU1.14: 6 residues within 4Å: Chain D: T.281, V.282, N.306, G.308, I.312 Ligands: CU1.13 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.281 CU1.15: 6 residues within 4Å: Chain E: H.38, M.42, F.50, N.103, R.104 Chain F: E.125 No protein-ligand interaction detected (PLIP) CU1.16: 4 residues within 4Å: Chain E: H.38, A.41, M.42, E.100 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:E.100 CU1.17: 3 residues within 4Å: Chain G: H.48, H.72, Q.404 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:H.48, G:H.72 CU1.18: 4 residues within 4Å: Chain G: H.33, H.137, H.139 Ligands: CU1.19 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:H.33 CU1.19: 4 residues within 4Å: Chain G: H.33, H.137, H.139 Ligands: CU1.18 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:H.137, G:H.139 CU1.20: 5 residues within 4Å: Chain G: E.316, R.323, Y.330, F.394, R.400 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:E.316 CU1.21: 3 residues within 4Å: Chain G: S.310, D.395 Ligands: CU1.22 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.395, G:D.395 CU1.22: 6 residues within 4Å: Chain G: T.281, V.282, N.306, G.308, I.312 Ligands: CU1.21 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:T.281 CU1.23: 6 residues within 4Å: Chain H: H.38, M.42, F.50, N.103, R.104 Chain I: E.125 No protein-ligand interaction detected (PLIP) CU1.24: 4 residues within 4Å: Chain H: H.38, A.41, M.42, E.100 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:E.100

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chang, W.H. et al., Copper Centers in the Cryo-EM Structure of Particulate Methane Monooxygenase Reveal the Catalytic Machinery of Methane Oxidation. J.Am.Chem.Soc. (2021)

Release Date

2021-07-21

Peptides

Particulate methane monooxygenase alpha subunit: ADG
Particulate methane monooxygenase beta subunit: BEH
Ammonia monooxygenase/methane monooxygenase, subunit C family protein: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
E

G
I

B
B

E
F

H
J

C
C

F
G

I
K

Membrane

We predict this structure to be a membrane protein.
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Particulate methane monooxygenase alpha subunit

Particulate methane monooxygenase beta subunit

Ammonia monooxygenase/methane monooxygenase, subunit C family protein

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