SMTL ID : 8sr2.1

particulate methane monooxygenase incubated with 4,4,4-trifluorobutanol

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

12 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.12: 4 residues within 4Å: Chain C: N.198, H.202, H.216 Ligands: CL.11 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.202, C:H.216 CU.13: 4 residues within 4Å: Chain C: D.127, H.131, R.136, H.144 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.127, C:H.131, C:H.144, H2O.5 CU.24: 3 residues within 4Å: Chain D: H.33, H.137, H.139 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.33, D:H.137, D:H.139 CU.25: 4 residues within 4Å: Chain D: H.48, H.72, F.74, Q.404 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:H.48, D:H.72 CU.27: 3 residues within 4Å: Chain E: H.33, H.137, H.139 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:H.33, E:H.137, E:H.139 CU.28: 4 residues within 4Å: Chain E: H.48, H.72, F.74, Q.404 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:H.48, E:H.72 CU.47: 4 residues within 4Å: Chain H: N.198, H.202, H.216 Ligands: CL.46 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:H.202, H:H.216 CU.48: 4 residues within 4Å: Chain H: D.127, H.131, R.136, H.144 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.127, H:H.131, H:H.144, H2O.15 CU.59: 4 residues within 4Å: Chain I: N.198, H.202, H.216 Ligands: CL.58 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:H.202, I:H.216 CU.60: 4 residues within 4Å: Chain I: D.127, H.131, R.136, H.144 4 PLIP interactions: 3 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:D.127, I:H.131, I:H.144, H2O.16

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

D10.3: 3 residues within 4Å: Chain A: V.248 Ligands: PLC.4, PLC.65 Ligand excluded by PLIP D10.6: 7 residues within 4Å: Chain B: F.229, M.230, F.233 Ligands: D10.7, D10.9, D10.34, P1O.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, D10.41, D10.44 Ligand excluded by PLIP D10.9: 5 residues within 4Å: Ligands: D10.6, D10.7, D10.34, D10.35, D10.44 Ligand excluded by PLIP D10.16: 5 residues within 4Å: Ligands: HXG.15, PLC.23, D10.51, HXG.62, D10.63 Ligand excluded by PLIP D10.26: 3 residues within 4Å: Chain D: V.248 Ligands: PLC.18, PLC.39 Ligand excluded by PLIP D10.29: 3 residues within 4Å: Chain E: V.248 Ligands: PLC.30, PLC.53 Ligand excluded by PLIP D10.32: 7 residues within 4Å: Chain F: F.229, M.230, F.233 Ligands: D10.33, D10.35, P1O.38, D10.43 Ligand excluded by PLIP D10.33: 7 residues within 4Å: Chain F: M.230, F.233, I.234, W.237 Ligands: D10.32, D10.34, D10.35 Ligand excluded by PLIP D10.34: 7 residues within 4Å: Chain F: W.237, F.238, R.242 Ligands: D10.6, D10.9, D10.33, P1O.37 Ligand excluded by PLIP D10.35: 5 residues within 4Å: Ligands: D10.9, D10.32, D10.33, D10.43, D10.44 Ligand excluded by PLIP D10.41: 7 residues within 4Å: Chain G: F.229, M.230, F.233 Ligands: D10.8, P1O.10, D10.42, D10.44 Ligand excluded by PLIP D10.42: 7 residues within 4Å: Chain G: M.230, F.233, I.234, W.237 Ligands: D10.41, D10.43, D10.44 Ligand excluded by PLIP D10.43: 7 residues within 4Å: Chain G: W.237, F.238, R.242 Ligands: D10.32, D10.35, P1O.38, D10.42 Ligand excluded by PLIP D10.44: 5 residues within 4Å: Ligands: D10.8, D10.9, D10.35, D10.41, D10.42 Ligand excluded by PLIP D10.51: 5 residues within 4Å: Ligands: HXG.15, D10.16, PLC.45, HXG.50, D10.63 Ligand excluded by PLIP D10.63: 5 residues within 4Å: Ligands: D10.16, PLC.36, HXG.50, D10.51, HXG.62 Ligand excluded by PLIP

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

PLC.4: 21 residues within 4Å: Chain A: I.244, V.248, M.251, N.255, T.261 Chain B: R.57, I.130, G.151, L.154, I.155, Y.157, P.158, W.161, A.213, P.214, A.217, F.218 Chain E: Y.381 Ligands: D10.3, PLC.64, PLC.65 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 G: L.59, T.62, V.63, I.66, V.67, T.204, F.219, M.223, I.227 Ligands: HXG.15, PLC.45 Ligand excluded by PLIP PLC.17: 28 residues within 4Å: Chain C: S.51, F.52, F.56, E.57, 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 G: M.150, G.209, K.210, D.211, P.214, V.215, F.218 Ligands: PLC.18, PLC.39 Ligand excluded by PLIP PLC.18: 11 residues within 4Å: Chain C: I.68, I.72, F.140, Y.149, P.153, L.192 Chain G: P.214, F.218 Ligands: PLC.17, D10.26, PLC.39 Ligand excluded by PLIP PLC.20: 17 residues within 4Å: Chain C: V.31, F.32, W.35, W.38, Y.39, Y.43, Y.59, F.63, T.66, E.67, L.70, E.71, T.74, L.150, I.154, I.157 Ligands: P1O.21 Ligand excluded by PLIP PLC.23: 16 residues within 4Å: Chain B: H.40, T.44, V.63, V.67, M.199, M.223 Chain C: L.210, V.212, Y.217, V.220, I.221, W.224 Ligands: HXG.15, D10.16, PLC.61, HXG.62 Ligand excluded by PLIP PLC.30: 21 residues within 4Å: Chain D: Y.381 Chain E: I.244, V.248, M.251, N.255, T.261 Chain F: R.57, I.130, G.151, L.154, I.155, Y.157, P.158, W.161, A.213, P.214, A.217, F.218 Ligands: D10.29, PLC.52, PLC.53 Ligand excluded by PLIP PLC.36: 13 residues within 4Å: Chain F: T.44, V.63, V.67, M.199, M.223 Chain I: V.212, Y.217, V.220, W.224 Ligands: PLC.49, HXG.50, HXG.62, D10.63 Ligand excluded by PLIP PLC.39: 21 residues within 4Å: Chain A: Y.381 Chain D: I.244, V.248, M.251, N.255, T.261 Chain G: R.57, I.130, G.151, L.154, I.155, Y.157, P.158, W.161, A.213, P.214, A.217, F.218 Ligands: PLC.17, PLC.18, D10.26 Ligand excluded by PLIP PLC.45: 14 residues within 4Å: Chain D: Q.145 Chain G: T.44, V.63, V.67, M.199, M.223 Chain H: V.212, Y.217, V.220, W.224 Ligands: PLC.14, HXG.15, HXG.50, D10.51 Ligand excluded by PLIP PLC.49: 21 residues within 4Å: Chain D: T.80 Chain F: L.59, T.62, V.63, I.66, V.67, T.204, F.219, M.223, I.227 Chain H: L.197, W.200, F.204, W.205, F.206, M.207, P.214, Y.217, G.218 Ligands: PLC.36, HXG.50 Ligand excluded by PLIP PLC.52: 28 residues within 4Å: Chain F: M.150, G.209, K.210, D.211, P.214, V.215, F.218 Chain H: S.51, F.52, F.56, E.57, 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.30, PLC.53 Ligand excluded by PLIP PLC.53: 11 residues within 4Å: Chain F: P.214, F.218 Chain H: I.68, I.72, F.140, Y.149, P.153, L.192 Ligands: D10.29, PLC.30, PLC.52 Ligand excluded by PLIP PLC.55: 17 residues within 4Å: Chain H: V.31, F.32, W.35, W.38, Y.39, Y.43, Y.59, F.63, T.66, E.67, L.70, E.71, T.74, L.150, I.154, I.157 Ligands: P1O.56 Ligand excluded by PLIP PLC.61: 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 E: T.80 Chain I: L.197, W.200, F.204, W.205, F.206, M.207, P.214, G.218 Ligands: PLC.23, HXG.62 Ligand excluded by PLIP PLC.64: 28 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, E.57, 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.65 Ligand excluded by PLIP PLC.65: 11 residues within 4Å: Chain B: P.214, F.218 Chain I: I.68, I.72, F.140, Y.149, P.153, L.192 Ligands: D10.3, PLC.4, PLC.64 Ligand excluded by PLIP PLC.67: 17 residues within 4Å: Chain I: V.31, F.32, W.35, W.38, Y.39, Y.43, Y.59, F.63, T.66, E.67, L.70, E.71, T.74, L.150, I.154, I.157 Ligands: P1O.68 Ligand excluded by PLIP

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

P1O.5: 11 residues within 4Å: Chain A: R.233 Chain B: V.134, L.137, S.138, G.139, S.140, F.143 Chain I: W.79, F.160, I.164 Ligands: P1O.69 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain I, 1 interactions with chain F Hydrophobic interactions: B:F.143, B:F.143, I:F.160, I:F.160 Hydrogen bonds: F:T.247 P1O.10: 19 residues within 4Å: Chain B: W.237, R.242, F.243, L.244, S.246, T.247 Chain C: L.179, L.182, V.183, V.186, G.187, L.225 Chain G: L.142, F.229, H.232, F.233, R.236 Ligands: D10.8, D10.41 10 PLIP interactions: 6 interactions with chain G, 1 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: G:L.142, G:F.229, G:F.229, G:F.233, C:L.182, B:W.237, B:W.237 Salt bridges: G:H.232, G:R.236, B:R.242 P1O.21: 21 residues within 4Å: Chain C: K.19, 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.20 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:W.21, C:W.21, C:F.24, C:W.108 Salt bridges: C:K.19, C:K.19 P1O.22: 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 G: S.140, L.142, F.143, I.146, V.147 Ligands: P1O.40 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:W.83, C:W.83, C:F.160, C:L.182, B:T.247 Salt bridges: C:K.167 P1O.31: 11 residues within 4Å: Chain E: R.233 Chain F: V.134, L.137, S.138, G.139, S.140, F.143 Chain H: W.79, F.160, I.164 Ligands: P1O.57 4 PLIP interactions: 2 interactions with chain H, 2 interactions with chain F Hydrophobic interactions: H:F.160, H:F.160, F:F.143, F:F.143 P1O.37: 20 residues within 4Å: Chain B: L.142, F.229, H.232, F.233, R.236 Chain F: 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, D10.34 10 PLIP interactions: 6 interactions with chain B, 3 interactions with chain F, 1 interactions with chain I Hydrophobic interactions: B:L.142, B:F.229, B:F.229, B:F.233, F:W.237, F:W.237, I:L.182 Salt bridges: B:H.232, B:R.236 Hydrogen bonds: F:Q.245 P1O.38: 19 residues within 4Å: Chain F: L.142, F.229, H.232, F.233, R.236 Chain G: W.237, R.242, F.243, L.244, S.246, T.247 Chain H: L.179, L.182, V.183, V.186, G.187, L.225 Ligands: D10.32, D10.43 9 PLIP interactions: 6 interactions with chain F, 1 interactions with chain H, 2 interactions with chain G Hydrophobic interactions: F:L.142, F:F.229, F:F.229, F:F.233, H:L.182, G:W.237, G:W.237 Salt bridges: F:H.232, F:R.236 P1O.40: 11 residues within 4Å: Chain C: W.79, F.160, I.164 Chain D: R.233 Chain G: V.134, L.137, S.138, G.139, S.140, F.143 Ligands: P1O.22 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain G Hydrophobic interactions: C:F.160, C:F.160, G:F.143, G:F.143 P1O.56: 21 residues within 4Å: Chain H: K.19, 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.55 6 PLIP interactions: 6 interactions with chain H Hydrophobic interactions: H:W.21, H:W.21, H:F.24, H:W.108 Salt bridges: H:K.19, H:K.19 P1O.57: 18 residues within 4Å: Chain F: S.140, L.142, F.143, I.146 Chain G: T.247 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.31 6 PLIP interactions: 5 interactions with chain H, 1 interactions with chain G Hydrophobic interactions: H:W.83, H:W.83, H:F.160, H:L.182, G:T.247 Salt bridges: H:K.167 P1O.68: 21 residues within 4Å: Chain I: K.19, 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.67 6 PLIP interactions: 6 interactions with chain I Hydrophobic interactions: I:W.21, I:W.21, I:F.24, I:W.108 Salt bridges: I:K.19, I:K.19 P1O.69: 19 residues within 4Å: Chain B: S.140, L.142, F.143, I.146, V.147 Chain F: 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 6 PLIP interactions: 5 interactions with chain I, 1 interactions with chain F Hydrophobic interactions: I:W.83, I:W.83, I:F.160, I:L.182, F:T.247 Salt bridges: I:K.167

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

CL.11: 3 residues within 4Å: Chain C: F.148, H.216 Ligands: CU.12 Ligand excluded by PLIP CL.46: 3 residues within 4Å: Chain H: F.148, H.216 Ligands: CU.47 Ligand excluded by PLIP CL.58: 3 residues within 4Å: Chain I: F.148, H.216 Ligands: CU.59 Ligand excluded by PLIP

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.14, D10.16, PLC.23, PLC.45, D10.51 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:W.205, C:W.205, C:P.214, C:Y.217 HXG.19: 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 C, 2 interactions with chain B Hydrophobic interactions: C:W.118, C:Y.122, B:I.102, B:F.106 HXG.50: 13 residues within 4Å: Chain D: Q.145, G.146 Chain H: W.205, F.206, M.207, E.208, P.214, Y.217 Ligands: PLC.36, PLC.45, PLC.49, D10.51, D10.63 5 PLIP interactions: 5 interactions with chain H Hydrophobic interactions: H:W.205, H:W.205, H:P.214, H:Y.217 Hydrogen bonds: H:W.205 HXG.54: 10 residues within 4Å: Chain G: 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 H, 2 interactions with chain G Hydrophobic interactions: H:W.118, H:Y.122, G:I.102, G:F.106 HXG.62: 13 residues within 4Å: Chain E: Q.145, G.146 Chain I: W.205, F.206, M.207, E.208, P.214, Y.217 Ligands: D10.16, PLC.23, PLC.36, PLC.61, D10.63 4 PLIP interactions: 4 interactions with chain I Hydrophobic interactions: I:W.205, I:W.205, I:P.214, I:Y.217 HXG.66: 10 residues within 4Å: Chain F: 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 I, 2 interactions with chain F Hydrophobic interactions: I:W.118, I:Y.122, F:I.102, F:F.106

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

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

Release Date

2023-11-15

Peptides

Particulate methane monooxygenase alpha subunit: ADE
Particulate methane monooxygenase beta subunit: BFG
Ammonia monooxygenase/methane monooxygenase, subunit C family protein: CHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
E

E
I

B
B

F
J

G
F

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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