SMTL ID : 7s4l.1

CryoEM structure of Methylotuvimicrobium alcaliphilum 20Z pMMO in a POPC nanodisc at 2.46 Angstrom resolution

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

9 x CU: COPPER (II) ION(Non-covalent)

CU.1: 3 residues within 4Å: Chain A: H.33, H.137, H.139 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.33, A:H.137, A:H.139 CU.2: 3 residues within 4Å: Chain A: H.48, H.72, M.404 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.48, A:H.72 CU.9: 4 residues within 4Å: Chain C: D.128, H.132, D.138, H.145 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.128, C:D.128, C:H.132, C:H.145 CU.15: 4 residues within 4Å: Chain D: D.128, H.132, D.138, H.145 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.128, D:H.132, D:H.145 CU.18: 4 residues within 4Å: Chain E: D.128, H.132, D.138, H.145 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.128, E:H.132, E:H.145 CU.33: 3 residues within 4Å: Chain H: H.33, H.137, H.139 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:H.33, H:H.137, H:H.139 CU.34: 3 residues within 4Å: Chain H: H.48, H.72, M.404 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:H.48, H:H.72 CU.35: 3 residues within 4Å: Chain I: H.33, H.137, H.139 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:H.33, I:H.137, I:H.139 CU.36: 3 residues within 4Å: Chain I: H.48, H.72, M.404 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:H.48, I:H.72

15 x HXG: 1,2-dihexanoyl-sn-glycero-3-phosphocholine(Non-covalent)(Covalent)

HXG.3: 13 residues within 4Å: Chain A: V.247, M.251, N.255, T.261 Chain B: L.154, Y.157, P.158, W.161, K.210, A.213, P.214, A.217, F.218 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.158 Salt bridges: B:K.210 HXG.4: 10 residues within 4Å: Chain B: W.237, K.242, V.244 Chain C: L.180, L.183 Chain G: M.141, F.229, F.233 Ligands: HXG.5, D10.31 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:F.229, G:F.229 HXG.5: 9 residues within 4Å: Chain B: F.233, F.234, S.236, W.237, G.239, S.240 Ligands: HXG.4, D10.6, D10.7 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.234, B:F.234, B:W.237, B:W.237, B:W.237 Salt bridges: B:K.242 HXG.10: 13 residues within 4Å: Chain C: I.24, Y.30, L.79, Y.82, K.85, R.89, R.102, T.105, T.108, W.109, M.112, Y.166, R.170 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:L.79, C:Y.82, C:W.109, C:W.109 Hydrogen bonds: C:T.105, C:Y.166 Salt bridges: C:R.102 HXG.11: 11 residues within 4Å: Chain C: S.52, F.53, F.57, M.62, Y.66, M.69, D.140 Chain G: F.208, P.214, V.215, F.218 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:D.140 HXG.16: 13 residues within 4Å: Chain D: I.24, Y.30, L.79, Y.82, K.85, R.89, R.102, T.105, T.108, W.109, M.112, Y.166, R.170 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:L.79, D:Y.82, D:W.109, D:W.109 Hydrogen bonds: D:T.105, D:Y.166 Salt bridges: D:R.102 HXG.17: 11 residues within 4Å: Chain B: F.208, P.214, V.215, F.218 Chain D: S.52, F.53, F.57, M.62, Y.66, M.69, D.140 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:D.140 HXG.19: 13 residues within 4Å: Chain E: I.24, Y.30, L.79, Y.82, K.85, R.89, R.102, T.105, T.108, W.109, M.112, Y.166, R.170 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:L.79, E:Y.82, E:W.109, E:W.109 Hydrogen bonds: E:T.105, E:Y.166 Salt bridges: E:R.102 HXG.20: 11 residues within 4Å: Chain E: S.52, F.53, F.57, M.62, Y.66, M.69, D.140 Chain F: F.208, P.214, V.215, F.218 1 PLIP interactions: 1 interactions with chain E Salt bridges: E:D.140 HXG.23: 14 residues within 4Å: Chain F: L.154, Y.157, P.158, W.161, K.210, A.213, P.214, A.217, F.218 Chain H: V.247, A.248, M.251, N.255, T.261 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:P.158 Salt bridges: F:K.210 HXG.24: 10 residues within 4Å: Chain B: M.141, F.229, F.233 Chain D: L.180, L.183 Chain F: W.237, K.242, V.244 Ligands: D10.6, HXG.25 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.229, B:F.229 HXG.25: 9 residues within 4Å: Chain F: F.233, F.234, S.236, W.237, G.239, S.240 Ligands: HXG.24, D10.26, D10.27 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:F.234, F:F.234, F:W.237, F:W.237, F:W.237 Salt bridges: F:K.242 HXG.28: 13 residues within 4Å: Chain G: L.154, Y.157, P.158, W.161, K.210, A.213, P.214, A.217, F.218 Chain I: V.247, M.251, N.255, T.261 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:P.158 Salt bridges: G:K.210 HXG.29: 10 residues within 4Å: Chain E: L.180, L.183 Chain F: M.141, F.229, F.233 Chain G: W.237, K.242, V.244 Ligands: D10.26, HXG.30 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:F.229, F:F.229 HXG.30: 9 residues within 4Å: Chain G: F.233, F.234, S.236, W.237, G.239, S.240 Ligands: HXG.29, D10.31, D10.32 6 PLIP interactions: 6 interactions with chain G Hydrophobic interactions: G:F.234, G:F.234, G:W.237, G:W.237, G:W.237 Salt bridges: G:K.242

9 x D10: DECANE(Non-covalent)(Non-functional Binders)

D10.6: 4 residues within 4Å: Chain B: F.233 Ligands: HXG.5, D10.7, HXG.24 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.233, B:F.233 D10.7: 4 residues within 4Å: Ligands: HXG.5, D10.6, D10.27, D10.32 No protein-ligand interaction detected (PLIP) D10.13: 4 residues within 4Å: Chain C: L.198, W.206, G.219 Ligands: 6ER.12 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.198, C:W.206, C:W.206 D10.14: 5 residues within 4Å: Chain D: L.198, W.206, P.215, G.219 Ligands: 6ER.8 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:L.198, D:W.206, D:W.206 D10.22: 4 residues within 4Å: Chain E: L.198, W.206, G.219 Ligands: 6ER.21 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:L.198, E:W.206, E:W.206 D10.26: 4 residues within 4Å: Chain F: F.233 Ligands: HXG.25, D10.27, HXG.29 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:F.233, F:F.233 D10.27: 4 residues within 4Å: Ligands: D10.7, HXG.25, D10.26, D10.32 No protein-ligand interaction detected (PLIP) D10.31: 4 residues within 4Å: Chain G: F.233 Ligands: HXG.4, HXG.30, D10.32 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:F.233, G:F.233 D10.32: 4 residues within 4Å: Ligands: D10.7, D10.27, HXG.30, D10.31 No protein-ligand interaction detected (PLIP)

3 x 6ER: (S)-2,3-bis(hexanoyloxy)propyl(2-(trimethylammonio)ethyl)phosphate(Non-covalent)

6ER.8: 12 residues within 4Å: Chain B: T.44, W.48, L.59, V.63, V.67, M.199 Chain C: V.213, Y.218 Chain D: W.201, F.205, W.206 Ligands: D10.14 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.48, B:V.63, B:V.63 6ER.12: 12 residues within 4Å: Chain C: W.201, F.205, W.206 Chain E: V.213, Y.218 Chain G: T.44, W.48, L.59, V.63, V.67, M.199 Ligands: D10.13 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:W.48, G:V.63, G:V.63 6ER.21: 12 residues within 4Å: Chain D: V.213, Y.218 Chain E: W.201, F.205, W.206 Chain F: T.44, W.48, L.59, V.63, V.67, M.199 Ligands: D10.22 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:W.48, F:V.63, F:V.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koo, C.W. et al., Recovery of particulate methane monooxygenase structure and activity in a lipid bilayer. Science (2022)

Release Date

2022-03-30

Peptides

Particulate methane monooxygenase, B subunit: AHI
Particulate methane monooxygenase, A subunit: BFG
Particulate methane monooxygenase, C subunit: CDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

H
D

I
E

B
B

F
F

G
G

C
C

D
H

E
I

Membrane

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

Particulate methane monooxygenase, A subunit

Particulate methane monooxygenase, C subunit

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