SMTL ID : 8sr1.1

particulate methane monooxygenase crosslinked with 4,4,4-trifluorobutanol 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.1, H.105, H.107 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.1, A:H.105, A:H.107 CU.2: 4 residues within 4Å: Chain A: H.16, H.40, F.42, Q.372 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.16, A:H.40 CU.12: 5 residues within 4Å: Chain C: N.183, H.187, L.200, H.201 Ligands: WIY.21 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.187, C:H.201 CU.23: 3 residues within 4Å: Chain D: H.1, H.105, H.107 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.1, D:H.105, D:H.107 CU.24: 4 residues within 4Å: Chain D: H.16, H.40, F.42, Q.372 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:H.16, D:H.40 CU.34: 3 residues within 4Å: Chain F: H.1, H.105, H.107 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:H.1, F:H.105, F:H.107 CU.35: 4 residues within 4Å: Chain F: H.16, H.40, F.42, Q.372 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:H.16, F:H.40 CU.46: 5 residues within 4Å: Chain H: N.183, H.187, L.200, H.201 Ligands: WIY.55 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:H.187, H:H.201 CU.57: 5 residues within 4Å: Chain I: N.183, H.187, L.200, H.201 Ligands: WIY.66 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:H.187, I:H.201

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

D10.3: 4 residues within 4Å: Chain A: I.212, V.216 Ligands: PLC.4, PLC.11 Ligand excluded by PLIP D10.6: 7 residues within 4Å: Chain B: F.223, M.224, F.227 Ligands: D10.7, D10.9, P1O.37, D10.42 Ligand excluded by PLIP D10.7: 7 residues within 4Å: Chain B: M.224, F.227, I.228, W.231 Ligands: D10.6, D10.8, D10.9 Ligand excluded by PLIP D10.8: 7 residues within 4Å: Chain B: W.231, F.232, R.236 Ligands: D10.7, P1O.10, D10.29, D10.32 Ligand excluded by PLIP D10.9: 5 residues within 4Å: Ligands: D10.6, D10.7, D10.32, D10.42, D10.43 Ligand excluded by PLIP D10.15: 5 residues within 4Å: Ligands: HXG.14, PLC.22, D10.49, HXG.59, D10.60 Ligand excluded by PLIP D10.25: 4 residues within 4Å: Chain D: I.212, V.216 Ligands: PLC.26, PLC.27 Ligand excluded by PLIP D10.29: 7 residues within 4Å: Chain E: F.223, M.224, F.227 Ligands: D10.8, P1O.10, D10.30, D10.32 Ligand excluded by PLIP D10.30: 7 residues within 4Å: Chain E: M.224, F.227, I.228, W.231 Ligands: D10.29, D10.31, D10.32 Ligand excluded by PLIP D10.31: 7 residues within 4Å: Chain E: W.231, F.232, R.236 Ligands: D10.30, P1O.33, D10.40, D10.43 Ligand excluded by PLIP D10.32: 5 residues within 4Å: Ligands: D10.8, D10.9, D10.29, D10.30, D10.43 Ligand excluded by PLIP D10.36: 4 residues within 4Å: Chain F: I.212, V.216 Ligands: PLC.38, PLC.44 Ligand excluded by PLIP D10.40: 7 residues within 4Å: Chain G: F.223, M.224, F.227 Ligands: D10.31, P1O.33, D10.41, D10.43 Ligand excluded by PLIP D10.41: 7 residues within 4Å: Chain G: M.224, F.227, I.228, W.231 Ligands: D10.40, D10.42, D10.43 Ligand excluded by PLIP D10.42: 7 residues within 4Å: Chain G: W.231, F.232, R.236 Ligands: D10.6, D10.9, P1O.37, D10.41 Ligand excluded by PLIP D10.43: 5 residues within 4Å: Ligands: D10.9, D10.31, D10.32, D10.40, D10.41 Ligand excluded by PLIP D10.49: 5 residues within 4Å: Ligands: HXG.14, D10.15, PLC.45, HXG.48, D10.60 Ligand excluded by PLIP D10.60: 5 residues within 4Å: Ligands: D10.15, HXG.48, D10.49, PLC.56, HXG.59 Ligand excluded by PLIP

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

PLC.4: 19 residues within 4Å: Chain A: V.216, M.219, N.223, T.229 Chain B: R.51, G.145, L.148, Y.151, P.152, W.155, K.204, A.207, P.208, A.211, F.212 Chain F: Y.349 Ligands: D10.3, PLC.11, PLC.61 Ligand excluded by PLIP PLC.11: 13 residues within 4Å: Chain B: K.204, P.208, F.212 Chain I: I.53, E.56, I.57, F.125, Y.134, P.138, L.177 Ligands: D10.3, PLC.4, PLC.61 Ligand excluded by PLIP PLC.13: 21 residues within 4Å: Chain A: T.48 Chain C: L.182, W.185, F.189, W.190, F.191, M.192, P.199, Y.202, G.203 Chain E: L.53, T.56, V.57, I.60, V.61, T.198, F.213, M.217, I.221 Ligands: HXG.14, PLC.45 Ligand excluded by PLIP PLC.16: 27 residues within 4Å: Chain C: S.36, F.37, F.41, M.46, L.49, Y.50, I.53, V.54, I.57, T.123, D.124, F.125, Y.134, L.177, P.178, V.180, G.181, E.184 Chain E: M.144, G.203, K.204, D.205, P.208, V.209, F.212 Ligands: PLC.26, PLC.27 Ligand excluded by PLIP PLC.18: 19 residues within 4Å: Chain C: I.13, V.16, F.17, W.20, W.23, Y.24, Y.28, Y.44, N.47, F.48, T.51, E.52, L.55, E.56, T.59, L.135, I.139, I.142 Ligands: P1O.19 Ligand excluded by PLIP PLC.22: 17 residues within 4Å: Chain A: Q.113 Chain B: T.38, V.57, V.61, M.193, M.217 Chain C: F.191, E.193, V.197, Y.202, V.205, I.206, W.209 Ligands: HXG.14, D10.15, PLC.58, HXG.59 Ligand excluded by PLIP PLC.26: 13 residues within 4Å: Chain C: I.53, E.56, I.57, F.125, Y.134, P.138, L.177 Chain E: K.204, P.208, F.212 Ligands: PLC.16, D10.25, PLC.27 Ligand excluded by PLIP PLC.27: 19 residues within 4Å: Chain A: Y.349 Chain D: V.216, M.219, N.223, T.229 Chain E: R.51, G.145, L.148, Y.151, P.152, W.155, K.204, A.207, P.208, A.211, F.212 Ligands: PLC.16, D10.25, PLC.26 Ligand excluded by PLIP PLC.38: 19 residues within 4Å: Chain D: Y.349 Chain F: V.216, M.219, N.223, T.229 Chain G: R.51, G.145, L.148, Y.151, P.152, W.155, K.204, A.207, P.208, A.211, F.212 Ligands: D10.36, PLC.44, PLC.50 Ligand excluded by PLIP PLC.44: 13 residues within 4Å: Chain G: K.204, P.208, F.212 Chain H: I.53, E.56, I.57, F.125, Y.134, P.138, L.177 Ligands: D10.36, PLC.38, PLC.50 Ligand excluded by PLIP PLC.45: 17 residues within 4Å: Chain D: Q.113 Chain E: T.38, V.57, V.61, M.193, M.217 Chain H: F.191, E.193, V.197, Y.202, V.205, I.206, W.209 Ligands: PLC.13, HXG.14, HXG.48, D10.49 Ligand excluded by PLIP PLC.47: 21 residues within 4Å: Chain D: T.48 Chain G: L.53, T.56, V.57, I.60, V.61, T.198, F.213, M.217, I.221 Chain H: L.182, W.185, F.189, W.190, F.191, M.192, P.199, Y.202, G.203 Ligands: HXG.48, PLC.56 Ligand excluded by PLIP PLC.50: 27 residues within 4Å: Chain G: M.144, G.203, K.204, D.205, P.208, V.209, F.212 Chain H: S.36, F.37, F.41, M.46, L.49, Y.50, I.53, V.54, I.57, T.123, D.124, F.125, Y.134, L.177, P.178, V.180, G.181, E.184 Ligands: PLC.38, PLC.44 Ligand excluded by PLIP PLC.52: 19 residues within 4Å: Chain H: I.13, V.16, F.17, W.20, W.23, Y.24, Y.28, Y.44, N.47, F.48, T.51, E.52, L.55, E.56, T.59, L.135, I.139, I.142 Ligands: P1O.53 Ligand excluded by PLIP PLC.56: 17 residues within 4Å: Chain F: Q.113 Chain G: T.38, V.57, V.61, M.193, M.217 Chain I: F.191, E.193, V.197, Y.202, V.205, I.206, W.209 Ligands: PLC.47, HXG.48, HXG.59, D10.60 Ligand excluded by PLIP PLC.58: 21 residues within 4Å: Chain B: L.53, T.56, V.57, I.60, V.61, T.198, F.213, M.217, I.221 Chain F: T.48 Chain I: L.182, W.185, F.189, W.190, F.191, M.192, P.199, Y.202, G.203 Ligands: PLC.22, HXG.59 Ligand excluded by PLIP PLC.61: 27 residues within 4Å: Chain B: M.144, G.203, K.204, D.205, P.208, V.209, F.212 Chain I: S.36, F.37, F.41, M.46, L.49, Y.50, I.53, V.54, I.57, T.123, D.124, F.125, Y.134, L.177, P.178, V.180, G.181, E.184 Ligands: PLC.4, PLC.11 Ligand excluded by PLIP PLC.63: 19 residues within 4Å: Chain I: I.13, V.16, F.17, W.20, W.23, Y.24, Y.28, Y.44, N.47, F.48, T.51, E.52, L.55, E.56, T.59, L.135, I.139, I.142 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.201, L.208 Chain B: V.128, L.131, S.132, G.133, S.134, F.137 Chain I: W.64, F.145, I.149 Ligands: P1O.65 4 PLIP interactions: 1 interactions with chain I, 3 interactions with chain B Hydrophobic interactions: I:F.145, B:F.137, B:F.137, B:F.137 P1O.10: 19 residues within 4Å: Chain B: W.231, R.236, F.237, L.238, Q.239, S.240, T.241 Chain C: L.164, L.167, V.168, V.171, L.210 Chain E: L.136, F.223, H.226, F.227, R.230 Ligands: D10.8, D10.29 10 PLIP interactions: 1 interactions with chain C, 5 interactions with chain E, 4 interactions with chain B Hydrophobic interactions: C:L.167, E:L.136, E:F.223, E:F.227, B:W.231, B:L.238 Salt bridges: E:H.226, E:R.230 Hydrogen bonds: B:Q.239, B:S.240 P1O.19: 20 residues within 4Å: Chain C: W.6, F.9, A.10, I.13, Y.14, T.59, L.63, Y.66, L.67, R.86, T.89, V.92, W.93, A.96, I.139, I.142, T.143, Y.150, R.154 Ligands: PLC.18 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:W.6, C:W.6, C:W.6, C:F.9, C:W.93, C:W.93 P1O.20: 19 residues within 4Å: Chain B: T.241 Chain C: S.61, W.64, G.65, W.68, F.145, F.148, I.149, K.152, I.162, L.167, V.171, F.174 Chain E: S.134, L.136, F.137, I.140, V.141 Ligands: P1O.28 8 PLIP interactions: 5 interactions with chain C, 1 interactions with chain B, 2 interactions with chain E Hydrophobic interactions: C:W.68, C:W.68, C:F.145, C:L.167, B:T.241, E:I.140, E:I.140 Salt bridges: C:K.152 P1O.28: 12 residues within 4Å: Chain C: W.64, F.145, I.149 Chain D: R.201, L.208 Chain E: V.128, L.131, S.132, G.133, S.134, F.137 Ligands: P1O.20 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain C Hydrophobic interactions: E:F.137, E:F.137, E:F.137, C:F.145 P1O.33: 19 residues within 4Å: Chain E: W.231, R.236, F.237, L.238, Q.239, S.240, T.241 Chain G: L.136, F.223, H.226, F.227, R.230 Chain H: L.164, L.167, V.168, V.171, L.210 Ligands: D10.31, D10.40 10 PLIP interactions: 5 interactions with chain G, 1 interactions with chain H, 4 interactions with chain E Hydrophobic interactions: G:L.136, G:F.223, G:F.227, H:L.167, E:W.231, E:L.238 Salt bridges: G:H.226, G:R.230 Hydrogen bonds: E:Q.239, E:S.240 P1O.37: 19 residues within 4Å: Chain B: L.136, F.223, H.226, F.227, R.230 Chain G: W.231, R.236, F.237, L.238, Q.239, S.240, T.241 Chain I: L.164, L.167, V.168, V.171, L.210 Ligands: D10.6, D10.42 9 PLIP interactions: 5 interactions with chain B, 3 interactions with chain G, 1 interactions with chain I Hydrophobic interactions: B:L.136, B:F.223, B:F.227, G:W.231, I:L.167 Salt bridges: B:H.226, B:R.230 Hydrogen bonds: G:Q.239, G:S.240 P1O.39: 12 residues within 4Å: Chain F: R.201, L.208 Chain G: V.128, L.131, S.132, G.133, S.134, F.137 Chain H: W.64, F.145, I.149 Ligands: P1O.54 4 PLIP interactions: 3 interactions with chain G, 1 interactions with chain H Hydrophobic interactions: G:F.137, G:F.137, G:F.137, H:F.145 P1O.53: 20 residues within 4Å: Chain H: W.6, F.9, A.10, I.13, Y.14, T.59, L.63, Y.66, L.67, R.86, T.89, V.92, W.93, A.96, I.139, I.142, T.143, Y.150, R.154 Ligands: PLC.52 6 PLIP interactions: 6 interactions with chain H Hydrophobic interactions: H:W.6, H:W.6, H:W.6, H:F.9, H:W.93, H:W.93 P1O.54: 19 residues within 4Å: Chain E: T.241 Chain G: S.134, L.136, F.137, I.140, V.141 Chain H: S.61, W.64, G.65, W.68, F.145, F.148, I.149, K.152, I.162, L.167, V.171, F.174 Ligands: P1O.39 8 PLIP interactions: 1 interactions with chain E, 5 interactions with chain H, 2 interactions with chain G Hydrophobic interactions: E:T.241, H:W.68, H:W.68, H:F.145, H:L.167, G:I.140, G:I.140 Salt bridges: H:K.152 P1O.64: 20 residues within 4Å: Chain I: W.6, F.9, A.10, I.13, Y.14, T.59, L.63, Y.66, L.67, R.86, T.89, V.92, W.93, A.96, I.139, I.142, T.143, Y.150, R.154 Ligands: PLC.63 6 PLIP interactions: 6 interactions with chain I Hydrophobic interactions: I:W.6, I:W.6, I:W.6, I:F.9, I:W.93, I:W.93 P1O.65: 19 residues within 4Å: Chain B: S.134, L.136, F.137, I.140, V.141 Chain G: T.241 Chain I: S.61, W.64, G.65, W.68, F.145, F.148, I.149, K.152, I.162, L.167, V.171, F.174 Ligands: P1O.5 6 PLIP interactions: 5 interactions with chain I, 1 interactions with chain G Hydrophobic interactions: I:W.68, I:W.68, I:F.145, I:L.167, G:T.241 Salt bridges: I:K.152

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

HXG.14: 14 residues within 4Å: Chain A: D.50, Q.113, G.114 Chain C: W.190, F.191, M.192, E.193, P.199, Y.202 Ligands: PLC.13, D10.15, PLC.22, PLC.45, D10.49 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:W.190, C:P.199, C:Y.202 Salt bridges: C:E.193 HXG.17: 10 residues within 4Å: Chain B: I.96, F.100 Chain C: L.19, R.22, W.23, G.26, W.99, Y.102, W.103, Y.107 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:L.19, C:W.103, B:I.96, B:F.100 HXG.48: 14 residues within 4Å: Chain D: D.50, Q.113, G.114 Chain H: W.190, F.191, M.192, E.193, P.199, Y.202 Ligands: PLC.45, PLC.47, D10.49, PLC.56, D10.60 4 PLIP interactions: 4 interactions with chain H Hydrophobic interactions: H:W.190, H:P.199, H:Y.202 Salt bridges: H:E.193 HXG.51: 10 residues within 4Å: Chain E: I.96, F.100 Chain H: L.19, R.22, W.23, G.26, W.99, Y.102, W.103, Y.107 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain H Hydrophobic interactions: E:I.96, E:F.100, H:L.19, H:W.103 HXG.59: 14 residues within 4Å: Chain F: D.50, Q.113, G.114 Chain I: W.190, F.191, M.192, E.193, P.199, Y.202 Ligands: D10.15, PLC.22, PLC.56, PLC.58, D10.60 4 PLIP interactions: 4 interactions with chain I Hydrophobic interactions: I:W.190, I:P.199, I:Y.202 Salt bridges: I:E.193 HXG.62: 10 residues within 4Å: Chain G: I.96, F.100 Chain I: L.19, R.22, W.23, G.26, W.99, Y.102, W.103, Y.107 4 PLIP interactions: 2 interactions with chain I, 2 interactions with chain G Hydrophobic interactions: I:L.19, I:W.103, G:I.96, G:F.100

3 x WIY: 4,4,4-trifluorobutan-1-ol(Covalent)

WIY.21: 12 residues within 4Å: Chain C: D.112, H.116, R.121, N.183, H.187, E.193, E.194, L.195, F.196, H.201 Chain E: R.200 Ligands: CU.12 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:H.116, C:F.196 WIY.55: 12 residues within 4Å: Chain G: R.200 Chain H: D.112, H.116, R.121, N.183, H.187, E.193, E.194, L.195, F.196, H.201 Ligands: CU.46 2 PLIP interactions: 2 interactions with chain H Hydrophobic interactions: H:H.116, H:F.196 WIY.66: 12 residues within 4Å: Chain B: R.200 Chain I: D.112, H.116, R.121, N.183, H.187, E.193, E.194, L.195, F.196, H.201 Ligands: CU.57 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:H.116, I:F.196

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

2023-11-15

Peptides

Particulate methane monooxygenase alpha subunit: ADF
Particulate methane monooxygenase beta subunit: BEG
Ammonia monooxygenase/methane monooxygenase, subunit C family protein: CHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
E

F
I

B
B

E
F

G
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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