SMTL ID : 8oyi.1

particulate methane monooxygenase with 2,2,2-trifluoroethanol bound

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: 4 residues within 4Å: Chain A: H.48, H.72, F.74, Q.404 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.48, A:H.72 CU.13: 5 residues within 4Å: Chain C: N.198, H.202, L.215, H.216 Ligands: ETF.22 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:H.202, C:H.216, ETF.22 CU.42: 3 residues within 4Å: Chain F: H.33, H.137, H.139 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:H.33, F:H.137, F:H.139 CU.43: 4 residues within 4Å: Chain F: H.48, H.72, F.74, Q.404 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:H.48, F:H.72 CU.45: 3 residues within 4Å: Chain G: H.33, H.137, H.139 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:H.33, G:H.137, G:H.139 CU.46: 4 residues within 4Å: Chain G: H.48, H.72, F.74, Q.404 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:H.48, G:H.72 CU.47: 5 residues within 4Å: Chain H: N.198, H.202, L.215, H.216 Ligands: ETF.56 3 PLIP interactions: 2 interactions with chain H, 1 Ligand-Ligand interactions Metal complexes: H:H.202, H:H.216, ETF.56 CU.57: 5 residues within 4Å: Chain I: N.198, H.202, L.215, H.216 Ligands: ETF.66 3 PLIP interactions: 2 interactions with chain I, 1 Ligand-Ligand interactions Metal complexes: I:H.202, I:H.216, ETF.66

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

D10.3: 4 residues within 4Å: Chain A: I.244, V.248 Ligands: PLC.4, PLC.12 Ligand excluded by PLIP D10.6: 7 residues within 4Å: Chain B: F.229, M.230, F.233 Ligands: D10.7, D10.9, P1O.32, D10.37 Ligand excluded by PLIP D10.7: 7 residues within 4Å: Chain B: M.230, F.233, I.234, W.237 Ligands: D10.6, D10.8, D10.9 Ligand excluded by PLIP D10.8: 7 residues within 4Å: Chain B: W.237, F.238, R.242 Ligands: D10.7, P1O.10, D10.27, D10.30 Ligand excluded by PLIP D10.9: 5 residues within 4Å: Ligands: D10.6, D10.7, D10.30, D10.37, D10.38 Ligand excluded by PLIP D10.16: 5 residues within 4Å: Ligands: PLC.11, HXG.15, D10.50, HXG.59, D10.60 Ligand excluded by PLIP D10.27: 7 residues within 4Å: Chain D: F.229, M.230, F.233 Ligands: D10.8, P1O.10, D10.28, D10.30 Ligand excluded by PLIP D10.28: 7 residues within 4Å: Chain D: M.230, F.233, I.234, W.237 Ligands: D10.27, D10.29, D10.30 Ligand excluded by PLIP D10.29: 7 residues within 4Å: Chain D: W.237, F.238, R.242 Ligands: D10.28, P1O.31, D10.35, D10.38 Ligand excluded by PLIP D10.30: 5 residues within 4Å: Ligands: D10.8, D10.9, D10.27, D10.28, D10.38 Ligand excluded by PLIP D10.35: 7 residues within 4Å: Chain E: F.229, M.230, F.233 Ligands: D10.29, P1O.31, D10.36, D10.38 Ligand excluded by PLIP D10.36: 7 residues within 4Å: Chain E: M.230, F.233, I.234, W.237 Ligands: D10.35, D10.37, D10.38 Ligand excluded by PLIP D10.37: 7 residues within 4Å: Chain E: W.237, F.238, R.242 Ligands: D10.6, D10.9, P1O.32, D10.36 Ligand excluded by PLIP D10.38: 5 residues within 4Å: Ligands: D10.9, D10.29, D10.30, D10.35, D10.36 Ligand excluded by PLIP D10.41: 4 residues within 4Å: Chain F: I.244, V.248 Ligands: PLC.24, PLC.25 Ligand excluded by PLIP D10.44: 4 residues within 4Å: Chain G: I.244, V.248 Ligands: PLC.33, PLC.40 Ligand excluded by PLIP D10.50: 5 residues within 4Å: Ligands: HXG.15, D10.16, PLC.23, HXG.49, D10.60 Ligand excluded by PLIP D10.60: 5 residues within 4Å: Ligands: D10.16, PLC.39, HXG.49, D10.50, HXG.59 Ligand excluded by PLIP

18 x PLC: DIUNDECYL PHOSPHATIDYL CHOLINE(Non-covalent)

PLC.4: 19 residues within 4Å: Chain A: V.248, M.251, N.255, T.261 Chain B: R.57, G.151, L.154, Y.157, P.158, W.161, K.210, A.213, P.214, A.217, F.218 Chain G: Y.381 Ligands: D10.3, PLC.12, PLC.61 Ligand excluded by PLIP PLC.11: 16 residues within 4Å: Chain A: Q.145 Chain B: T.44, V.63, V.67, M.199, M.223 Chain C: E.208, V.212, Y.217, V.220, I.221, W.224 Ligands: HXG.15, D10.16, PLC.58, HXG.59 Ligand excluded by PLIP PLC.12: 13 residues within 4Å: Chain B: K.210, P.214, F.218 Chain I: I.68, E.71, I.72, F.140, Y.149, P.153, L.192 Ligands: D10.3, PLC.4, PLC.61 Ligand excluded by PLIP PLC.14: 20 residues within 4Å: Chain A: T.80 Chain C: L.197, W.200, F.204, W.205, F.206, M.207, P.214, G.218 Chain D: L.59, T.62, V.63, I.66, V.67, T.204, F.219, M.223, I.227 Ligands: HXG.15, PLC.23 Ligand excluded by PLIP PLC.17: 27 residues within 4Å: Chain C: S.51, F.52, F.56, M.61, L.64, Y.65, I.68, V.69, I.72, T.138, D.139, F.140, Y.149, L.192, P.193, V.195, G.196, E.199 Chain D: M.150, G.209, K.210, D.211, P.214, V.215, F.218 Ligands: PLC.24, PLC.25 Ligand excluded by PLIP PLC.19: 19 residues within 4Å: Chain C: I.28, V.31, F.32, W.35, W.38, Y.39, Y.43, Y.59, N.62, F.63, T.66, E.67, L.70, E.71, T.74, L.150, I.154, I.157 Ligands: P1O.20 Ligand excluded by PLIP PLC.23: 16 residues within 4Å: Chain D: T.44, V.63, V.67, M.199, M.223 Chain F: Q.145 Chain H: E.208, V.212, Y.217, V.220, I.221, W.224 Ligands: PLC.14, HXG.15, HXG.49, D10.50 Ligand excluded by PLIP PLC.24: 13 residues within 4Å: Chain C: I.68, E.71, I.72, F.140, Y.149, P.153, L.192 Chain D: K.210, P.214, F.218 Ligands: PLC.17, PLC.25, D10.41 Ligand excluded by PLIP PLC.25: 19 residues within 4Å: Chain A: Y.381 Chain D: R.57, G.151, L.154, Y.157, P.158, W.161, K.210, A.213, P.214, A.217, F.218 Chain F: V.248, M.251, N.255, T.261 Ligands: PLC.17, PLC.24, D10.41 Ligand excluded by PLIP PLC.33: 19 residues within 4Å: Chain E: R.57, G.151, L.154, Y.157, P.158, W.161, K.210, A.213, P.214, A.217, F.218 Chain F: Y.381 Chain G: V.248, M.251, N.255, T.261 Ligands: PLC.40, D10.44, PLC.51 Ligand excluded by PLIP PLC.39: 16 residues within 4Å: Chain E: T.44, V.63, V.67, M.199, M.223 Chain G: Q.145 Chain I: E.208, V.212, Y.217, V.220, I.221, W.224 Ligands: PLC.48, HXG.49, HXG.59, D10.60 Ligand excluded by PLIP PLC.40: 13 residues within 4Å: Chain E: K.210, P.214, F.218 Chain H: I.68, E.71, I.72, F.140, Y.149, P.153, L.192 Ligands: PLC.33, D10.44, PLC.51 Ligand excluded by PLIP PLC.48: 20 residues within 4Å: Chain E: L.59, T.62, V.63, I.66, V.67, T.204, F.219, M.223, I.227 Chain F: T.80 Chain H: L.197, W.200, F.204, W.205, F.206, M.207, P.214, G.218 Ligands: PLC.39, HXG.49 Ligand excluded by PLIP PLC.51: 27 residues within 4Å: Chain E: M.150, G.209, K.210, D.211, P.214, V.215, F.218 Chain H: S.51, F.52, F.56, M.61, L.64, Y.65, I.68, V.69, I.72, T.138, D.139, F.140, Y.149, L.192, P.193, V.195, G.196, E.199 Ligands: PLC.33, PLC.40 Ligand excluded by PLIP PLC.53: 19 residues within 4Å: Chain H: I.28, V.31, F.32, W.35, W.38, Y.39, Y.43, Y.59, N.62, F.63, T.66, E.67, L.70, E.71, T.74, L.150, I.154, I.157 Ligands: P1O.54 Ligand excluded by PLIP PLC.58: 20 residues within 4Å: Chain B: L.59, T.62, V.63, I.66, V.67, T.204, F.219, M.223, I.227 Chain G: T.80 Chain I: L.197, W.200, F.204, W.205, F.206, M.207, P.214, G.218 Ligands: PLC.11, HXG.59 Ligand excluded by PLIP PLC.61: 27 residues within 4Å: Chain B: M.150, G.209, K.210, D.211, P.214, V.215, F.218 Chain I: S.51, F.52, F.56, M.61, L.64, Y.65, I.68, V.69, I.72, T.138, D.139, F.140, Y.149, L.192, P.193, V.195, G.196, E.199 Ligands: PLC.4, PLC.12 Ligand excluded by PLIP PLC.63: 19 residues within 4Å: Chain I: I.28, V.31, F.32, W.35, W.38, Y.39, Y.43, Y.59, N.62, F.63, T.66, E.67, L.70, E.71, T.74, L.150, I.154, I.157 Ligands: P1O.64 Ligand excluded by PLIP

12 x P1O: 1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

P1O.5: 12 residues within 4Å: Chain A: R.233, L.240 Chain B: V.134, L.137, S.138, G.139, S.140, F.143 Chain I: W.79, F.160, I.164 Ligands: P1O.65 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain I Hydrophobic interactions: B:F.143, B:F.143, B:F.143, I:F.160 P1O.10: 19 residues within 4Å: Chain B: W.237, R.242, F.243, L.244, Q.245, S.246, T.247 Chain C: L.179, L.182, V.183, V.186, L.225 Chain D: L.142, F.229, H.232, F.233, R.236 Ligands: D10.8, D10.27 10 PLIP interactions: 5 interactions with chain D, 4 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: D:L.142, D:F.229, D:F.233, B:W.237, B:L.244, C:L.182 Salt bridges: D:H.232, D:R.236 Hydrogen bonds: B:Q.245, B:S.246 P1O.20: 20 residues within 4Å: Chain C: W.21, F.24, A.25, I.28, Y.29, T.74, L.78, Y.81, L.82, R.101, T.104, V.107, W.108, A.111, I.154, I.157, T.158, Y.165, R.169 Ligands: PLC.19 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:W.21, C:W.21, C:W.21, C:F.24, C:W.108, C:W.108 Hydrogen bonds: C:Y.165 P1O.21: 19 residues within 4Å: Chain B: T.247 Chain C: S.76, W.79, G.80, W.83, F.160, F.163, I.164, K.167, I.177, L.182, V.186, F.189 Chain D: S.140, L.142, F.143, I.146, V.147 Ligands: P1O.26 8 PLIP interactions: 2 interactions with chain D, 5 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: D:I.146, D:I.146, C:W.83, C:W.83, C:F.160, C:L.182, B:T.247 Salt bridges: C:K.167 P1O.26: 12 residues within 4Å: Chain C: W.79, F.160, I.164 Chain D: V.134, L.137, S.138, G.139, S.140, F.143 Chain F: R.233, L.240 Ligands: P1O.21 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:F.143, D:F.143, D:F.143, C:F.160 P1O.31: 19 residues within 4Å: Chain D: W.237, R.242, F.243, L.244, Q.245, S.246, T.247 Chain E: L.142, F.229, H.232, F.233, R.236 Chain H: L.179, L.182, V.183, V.186, L.225 Ligands: D10.29, D10.35 10 PLIP interactions: 5 interactions with chain E, 4 interactions with chain D, 1 interactions with chain H Hydrophobic interactions: E:L.142, E:F.229, E:F.233, D:W.237, D:L.244, H:L.182 Salt bridges: E:H.232, E:R.236 Hydrogen bonds: D:Q.245, D:S.246 P1O.32: 20 residues within 4Å: Chain B: L.142, F.229, H.232, F.233, R.236 Chain E: W.237, R.242, F.243, L.244, Q.245, S.246, T.247 Chain I: L.179, L.182, V.183, V.186, G.187, L.225 Ligands: D10.6, D10.37 9 PLIP interactions: 3 interactions with chain E, 5 interactions with chain B, 1 interactions with chain I Hydrophobic interactions: E:W.237, B:L.142, B:F.229, B:F.233, I:L.182 Hydrogen bonds: E:Q.245, E:S.246 Salt bridges: B:H.232, B:R.236 P1O.34: 12 residues within 4Å: Chain E: V.134, L.137, S.138, G.139, S.140, F.143 Chain G: R.233, L.240 Chain H: W.79, F.160, I.164 Ligands: P1O.55 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain H Hydrophobic interactions: E:F.143, E:F.143, E:F.143, H:F.160 P1O.54: 20 residues within 4Å: Chain H: W.21, F.24, A.25, I.28, Y.29, T.74, L.78, Y.81, L.82, R.101, T.104, V.107, W.108, A.111, I.154, I.157, T.158, Y.165, R.169 Ligands: PLC.53 7 PLIP interactions: 7 interactions with chain H Hydrophobic interactions: H:W.21, H:W.21, H:W.21, H:F.24, H:W.108, H:W.108 Hydrogen bonds: H:Y.165 P1O.55: 19 residues within 4Å: Chain D: T.247 Chain E: S.140, L.142, F.143, I.146, V.147 Chain H: S.76, W.79, G.80, W.83, F.160, F.163, I.164, K.167, I.177, L.182, V.186, F.189 Ligands: P1O.34 8 PLIP interactions: 5 interactions with chain H, 2 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: H:W.83, H:W.83, H:F.160, H:L.182, E:I.146, E:I.146, D:T.247 Salt bridges: H:K.167 P1O.64: 20 residues within 4Å: Chain I: W.21, F.24, A.25, I.28, Y.29, T.74, L.78, Y.81, L.82, R.101, T.104, V.107, W.108, A.111, I.154, I.157, T.158, Y.165, R.169 Ligands: PLC.63 7 PLIP interactions: 7 interactions with chain I Hydrophobic interactions: I:W.21, I:W.21, I:W.21, I:F.24, I:W.108, I:W.108 Hydrogen bonds: I:Y.165 P1O.65: 19 residues within 4Å: Chain B: S.140, L.142, F.143, I.146, V.147 Chain E: T.247 Chain I: S.76, W.79, G.80, W.83, F.160, F.163, I.164, K.167, I.177, L.182, V.186, F.189 Ligands: P1O.5 8 PLIP interactions: 5 interactions with chain I, 2 interactions with chain B, 1 interactions with chain E Hydrophobic interactions: I:W.83, I:W.83, I:F.160, I:L.182, B:I.146, B:I.146, E:T.247 Salt bridges: I:K.167

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

HXG.15: 14 residues within 4Å: Chain A: D.82, Q.145, G.146 Chain C: W.205, F.206, M.207, E.208, P.214, Y.217 Ligands: PLC.11, PLC.14, D10.16, PLC.23, D10.50 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:W.205, C:P.214, C:Y.217 Salt bridges: C:E.208 HXG.18: 10 residues within 4Å: Chain B: I.102, F.106 Chain C: L.34, R.37, W.38, G.41, W.114, Y.117, W.118, Y.122 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:I.102, B:F.106, C:L.34, C:W.118 HXG.49: 14 residues within 4Å: Chain F: D.82, Q.145, G.146 Chain H: W.205, F.206, M.207, E.208, P.214, Y.217 Ligands: PLC.23, PLC.39, PLC.48, D10.50, D10.60 4 PLIP interactions: 4 interactions with chain H Hydrophobic interactions: H:W.205, H:P.214, H:Y.217 Salt bridges: H:E.208 HXG.52: 10 residues within 4Å: Chain D: I.102, F.106 Chain H: L.34, R.37, W.38, G.41, W.114, Y.117, W.118, Y.122 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain H Hydrophobic interactions: D:I.102, D:F.106, H:L.34, H:W.118 HXG.59: 14 residues within 4Å: Chain G: D.82, Q.145, G.146 Chain I: W.205, F.206, M.207, E.208, P.214, Y.217 Ligands: PLC.11, D10.16, PLC.39, PLC.58, D10.60 4 PLIP interactions: 4 interactions with chain I Hydrophobic interactions: I:W.205, I:P.214, I:Y.217 Salt bridges: I:E.208 HXG.62: 10 residues within 4Å: Chain E: I.102, F.106 Chain I: L.34, R.37, W.38, G.41, W.114, Y.117, W.118, Y.122 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain I Hydrophobic interactions: E:I.102, E:F.106, I:L.34, I:W.118

3 x ETF: TRIFLUOROETHANOL(Non-covalent)

ETF.22: 13 residues within 4Å: Chain B: L.43 Chain C: T.124, D.127, G.128, H.144, E.147, F.148, N.198, H.202, F.211, H.216, F.219 Ligands: CU.13 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.198 Water bridges: C:R.136 Halogen bonds: C:E.147 ETF.56: 13 residues within 4Å: Chain D: L.43 Chain H: T.124, D.127, G.128, H.144, E.147, F.148, N.198, H.202, F.211, H.216, F.219 Ligands: CU.47 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:N.198 Water bridges: H:R.136 Halogen bonds: H:E.147 ETF.66: 13 residues within 4Å: Chain E: L.43 Chain I: T.124, D.127, G.128, H.144, E.147, F.148, N.198, H.202, F.211, H.216, F.219 Ligands: CU.57 3 PLIP interactions: 3 interactions with chain I Hydrogen bonds: I:N.198 Water bridges: I:R.136 Halogen bonds: I:E.147

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tucci, F.J. et al., Product analog binding identifies the copper active site of particulate methane monooxygenase. Nat Catal (2023)

Release Date

2023-11-08

Peptides

Particulate methane monooxygenase alpha subunit: AFG
Particulate methane monooxygenase beta subunit: BDE
Ammonia monooxygenase/methane monooxygenase, subunit C family protein: CHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

F
E

G
I

B
B

D
F

E
J

C
C

H
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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