SMTL ID : 8q54.1

N5-methyl-H4MPT:CoM methyltransferase -coenzyme M complex + CoM

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-3-3-3-mer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain B: A.97, L.100 Chain H: L.235, L.236, V.238 5 PLIP interactions: 1 interactions with chain H, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: H:L.235, B:A.97, H2O.1, H2O.1, H2O.2 MG.9: 3 residues within 4Å: Chain I: A.97, L.100 Chain O: L.235 5 PLIP interactions: 1 interactions with chain I, 1 interactions with chain O, 3 Ligand-Water interactions Metal complexes: I:A.97, O:L.235, H2O.2, H2O.2, H2O.3 MG.17: 6 residues within 4Å: Chain A: L.235, L.236, V.238 Chain P: A.97, L.98, L.100 5 PLIP interactions: 1 interactions with chain P, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: P:A.97, A:L.235, H2O.1, H2O.3, H2O.3

12 x JCV: [(2~{S},7~{R},11~{R},15~{S},19~{S},22~{S},26~{S},30~{R},34~{R},39~{S},43~{R},47~{R},51~{S},55~{S},58~{S},62~{S},66~{R},70~{R})-39-[[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]-7,11,15,19,22,26,30,34,43,47,51,55,58,62,66,70-hexadecamethyl-1,4,37,40-tetraoxacyclodoheptacont-2-yl]methyl [(2~{R},3~{S},5~{R},6~{R})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl] hydrogen phosphate(Non-covalent)

JCV.2: 36 residues within 4Å: Chain C: I.210, A.213, I.214, L.217, W.226, W.227, S.230, L.231, A.234, W.237, I.238, F.241, R.242, V.245, S.246, F.249, W.257 Chain E: I.97, M.100, T.103, T.104, V.107, M.111, M.126, V.130, L.133 Chain T: I.42, S.43, A.46, L.50, V.53, L.54, M.61, L.65 Ligands: JCV.6, JCV.23 18 PLIP interactions: 4 interactions with chain E, 3 interactions with chain T, 11 interactions with chain C Hydrophobic interactions: E:T.103, E:V.107, E:V.130, E:L.133, T:I.42, T:A.46, T:L.50, C:I.210, C:I.214, C:W.227, C:W.227, C:W.227, C:L.231, C:W.237, C:W.237, C:F.241, C:F.241 Hydrogen bonds: C:W.227 JCV.6: 43 residues within 4Å: Chain A: Q.220, M.223, I.224, A.227, F.228, T.231, L.235 Chain C: L.217, I.220, W.226 Chain E: L.79, S.82, M.83, Q.84, L.85, I.93, V.96, I.97, A.99, M.100, T.103, Q.131, L.133, G.134, A.137 Chain G: R.43, Q.46, Q.47, R.50 Chain P: L.90, I.94, L.98 Chain T: F.34, I.38, R.41, I.42, I.45, A.46, F.49, L.50, V.53 Ligands: JCV.2, JCV.22 18 PLIP interactions: 6 interactions with chain T, 3 interactions with chain E, 1 interactions with chain P, 4 interactions with chain G, 2 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: T:I.42, T:F.49, T:F.49, T:F.49, T:L.50, E:M.83, E:L.85, E:A.137, P:I.94, A:F.228, C:I.220, C:W.226 Salt bridges: T:R.41, G:R.50 Hydrogen bonds: G:R.43, G:R.43, G:R.50, A:Q.220 JCV.7: 50 residues within 4Å: Chain A: F.211, Y.215, K.218, V.219, I.222, L.226 Chain B: V.85, Y.86, I.89, L.90, I.93, F.96 Chain E: L.13, A.17, I.20, A.23, A.24, L.27, V.87, I.88, H.139, I.142, F.145, C.146, G.149, Y.152, L.153, L.156, H.229, A.232, K.233, P.237 Chain F: F.34, L.37, R.41, I.45 Chain G: Y.56, I.60, I.63, I.64, V.67, T.68 Chain H: I.224, F.228, L.236 Chain N: Q.47, R.50, I.54, I.58 Ligands: JCV.16 29 PLIP interactions: 3 interactions with chain A, 9 interactions with chain E, 2 interactions with chain G, 6 interactions with chain B, 1 interactions with chain F, 3 interactions with chain H, 5 interactions with chain N Hydrophobic interactions: A:V.219, A:L.226, E:A.23, E:I.88, E:I.142, E:F.145, E:L.153, G:I.63, G:I.64, B:Y.86, B:I.89, B:I.89, B:L.90, B:I.93, H:F.228, H:F.228, H:F.228, N:I.58 Hydrogen bonds: A:K.218, E:Y.152, E:H.229, E:A.232, E:K.233, B:Y.86, N:Q.47, N:Q.47, N:R.50 Salt bridges: F:R.41, N:R.50 JCV.8: 33 residues within 4Å: Chain B: T.77, K.80, L.81, I.84 Chain D: L.86, V.87, L.90, F.94 Chain E: F.241, A.245, L.249, W.252, F.257, T.260, G.261, I.264, S.265, I.268, I.269, L.273, L.276, R.279, L.280, F.283, R.287 Chain F: I.47, L.51, L.54, L.55, V.58, P.59, I.68 Ligands: JCV.10 18 PLIP interactions: 2 interactions with chain D, 11 interactions with chain E, 3 interactions with chain B, 2 interactions with chain F Hydrophobic interactions: D:V.87, D:L.90, E:F.241, E:A.245, E:L.249, E:F.257, E:F.257, E:I.264, E:I.268, E:L.273, E:L.276, E:R.279, B:L.81, F:P.59, F:I.68 Salt bridges: E:R.287 Hydrogen bonds: B:T.77, B:K.80 JCV.10: 40 residues within 4Å: Chain B: L.95, L.98, L.99 Chain F: I.42, S.43, A.46, L.50, V.53, G.57, M.61, I.64, L.65 Chain J: I.210, A.213, I.214, L.217, W.226, W.227, S.230, L.231, A.234, W.237, I.238, F.241, R.242, V.245, S.246, F.249, W.257 Chain L: M.100, T.103, T.104, V.107, M.111, M.126, L.129, V.130, L.133 Ligands: JCV.8, JCV.16 15 PLIP interactions: 7 interactions with chain J, 4 interactions with chain F, 2 interactions with chain B, 2 interactions with chain L Hydrophobic interactions: J:I.210, J:W.227, J:L.231, J:W.237, J:I.238, J:F.241, J:F.241, F:I.42, F:A.46, F:L.50, F:V.53, B:L.98, B:L.99, L:T.103, L:V.107 JCV.14: 50 residues within 4Å: Chain H: F.211, Y.215, K.218, V.219, I.222, L.226 Chain I: V.85, Y.86, I.89, L.90, I.93, F.96 Chain L: L.13, A.17, I.20, A.23, A.24, L.27, V.87, I.88, H.139, I.142, F.145, C.146, G.149, Y.152, L.153, L.156, H.229, A.232, K.233, P.237 Chain M: F.34, L.37, R.41, I.45 Chain N: Y.56, I.60, I.63, I.64, V.67, T.68 Chain O: I.224, F.228, L.236 Chain U: Q.47, R.50, I.54, I.58 Ligands: JCV.24 30 PLIP interactions: 5 interactions with chain N, 5 interactions with chain U, 6 interactions with chain L, 3 interactions with chain H, 7 interactions with chain I, 3 interactions with chain O, 1 interactions with chain M Hydrophobic interactions: N:I.60, N:I.63, N:I.64, N:I.64, N:T.68, U:I.58, L:A.23, L:F.145, L:L.153, H:V.219, H:L.226, I:Y.86, I:I.89, I:L.90, I:L.90, I:I.93, I:F.96, O:I.224, O:F.228, O:F.228 Hydrogen bonds: U:Q.47, U:Q.47, U:R.50, L:A.232, L:K.233, H:K.218, I:Y.86 Salt bridges: U:R.50, M:R.41 Water bridges: L:I.88 JCV.15: 29 residues within 4Å: Chain I: T.77, K.80, L.81, I.84 Chain K: I.83, L.86, L.90, F.94 Chain L: F.241, A.245, L.249, W.252, F.257, T.260, G.261, I.264, S.265, I.268, I.269, L.273, L.276, L.280, F.283, R.287 Chain M: I.47, L.51, L.55, I.68 Ligands: JCV.18 14 PLIP interactions: 4 interactions with chain I, 2 interactions with chain K, 8 interactions with chain L Hydrophobic interactions: I:K.80, I:L.81, I:I.84, K:L.86, K:L.90, L:F.241, L:F.257, L:F.257, L:F.257, L:I.268, L:F.283, L:F.283 Hydrogen bonds: I:K.80 Salt bridges: L:R.287 JCV.16: 44 residues within 4Å: Chain B: L.90, I.94, L.98 Chain F: F.34, I.38, R.41, I.42, I.45, A.46, F.49, L.50, V.53 Chain H: Q.220, M.223, I.224, A.227, F.228, L.235 Chain J: L.217, I.220, G.221, W.226 Chain L: L.79, S.82, M.83, Q.84, L.85, M.89, I.93, V.96, I.97, A.99, M.100, T.103, Q.131, L.133, G.134, A.137 Chain N: R.43, Q.46, Q.47, R.50 Ligands: JCV.7, JCV.10 19 PLIP interactions: 5 interactions with chain F, 5 interactions with chain L, 4 interactions with chain N, 3 interactions with chain J, 2 interactions with chain H Hydrophobic interactions: F:I.42, F:I.45, F:A.46, F:F.49, L:L.79, L:L.85, L:L.85, L:V.96, L:A.137, J:L.217, J:W.226, J:W.226, H:L.235 Salt bridges: F:R.41, N:R.50 Hydrogen bonds: N:R.43, N:R.43, N:Q.46, H:Q.220 JCV.18: 34 residues within 4Å: Chain M: I.42, S.43, A.46, L.50, M.61, L.65 Chain Q: I.210, A.213, I.214, L.217, P.224, W.226, W.227, S.230, L.231, A.234, L.235, W.237, I.238, F.241, V.245, S.246, F.249, W.257 Chain S: M.100, T.103, T.104, V.107, M.111, M.126, V.130, L.133 Ligands: JCV.15, JCV.24 16 PLIP interactions: 12 interactions with chain Q, 2 interactions with chain S, 2 interactions with chain M Hydrophobic interactions: Q:I.210, Q:L.217, Q:W.227, Q:W.227, Q:W.227, Q:L.231, Q:L.231, Q:L.235, Q:W.237, Q:F.241, Q:F.241, S:T.103, S:V.130, M:A.46, M:L.65 Hydrogen bonds: Q:W.227 JCV.22: 50 residues within 4Å: Chain A: I.224, F.228, L.236 Chain G: Q.47, R.50, I.54, I.58 Chain O: F.211, Y.215, K.218, V.219, I.222, L.226 Chain P: V.85, Y.86, I.89, L.90, I.93, F.96 Chain S: L.13, A.17, I.20, A.23, A.24, L.27, V.87, I.88, I.91, H.139, I.142, F.145, C.146, G.149, Y.152, L.153, L.156, H.229, A.232, K.233, P.237 Chain T: F.34, L.37, R.41, I.45 Chain U: Y.56, I.60, I.64, V.67, T.68 Ligands: JCV.6 22 PLIP interactions: 3 interactions with chain A, 6 interactions with chain S, 4 interactions with chain P, 4 interactions with chain G, 4 interactions with chain O, 1 interactions with chain T Hydrophobic interactions: A:I.224, A:F.228, A:F.228, S:A.23, S:F.145, S:L.153, P:L.90, P:I.93, P:F.96, G:I.58, O:K.218, O:L.226 Hydrogen bonds: S:H.229, S:A.232, S:K.233, P:Y.86, G:Q.47, G:R.50, O:F.211, O:K.218 Salt bridges: G:R.50, T:R.41 JCV.23: 32 residues within 4Å: Chain P: T.77, K.80, L.81, I.84 Chain R: L.86, L.90, F.94 Chain S: F.241, A.245, L.249, W.252, F.257, G.261, I.264, S.265, I.268, I.269, L.273, L.276, R.279, L.280, F.283, R.287 Chain T: I.47, L.50, L.51, L.54, L.55, V.58, P.59, I.68 Ligands: JCV.2 24 PLIP interactions: 12 interactions with chain S, 6 interactions with chain T, 2 interactions with chain R, 4 interactions with chain P Hydrophobic interactions: S:F.241, S:L.249, S:W.252, S:F.257, S:I.268, S:I.269, S:L.276, S:F.283, T:I.47, T:L.51, T:L.51, T:L.54, T:L.54, T:P.59, R:L.86, R:L.90, P:T.77, P:K.80, P:L.81, P:I.84 Hydrogen bonds: S:F.257 Water bridges: S:R.287, S:R.287 Salt bridges: S:R.287 JCV.24: 49 residues within 4Å: Chain I: L.90, I.94, L.98, L.99, L.100 Chain L: M.1, I.5 Chain M: F.34, I.38, R.41, I.42, I.45, A.46, F.49, L.50, V.53, I.64 Chain O: Q.220, M.223, I.224, A.227, F.228, T.231, L.232, L.235, V.238 Chain Q: L.217, I.220, W.226 Chain S: L.79, M.83, L.85, M.89, I.93, V.96, I.97, A.99, M.100, T.103, Q.131, L.133, G.134, A.137 Chain U: R.43, Q.46, Q.47, R.50 Ligands: JCV.14, JCV.18 17 PLIP interactions: 2 interactions with chain Q, 3 interactions with chain U, 4 interactions with chain S, 4 interactions with chain M, 3 interactions with chain O, 1 interactions with chain I Hydrophobic interactions: Q:L.217, Q:W.226, S:L.85, S:L.85, S:I.93, S:V.96, M:F.49, M:F.49, M:F.49, O:V.238 Hydrogen bonds: U:R.43, U:R.43, O:Q.220, O:Q.220, I:L.100 Salt bridges: U:R.50, M:R.41

6 x NA: SODIUM ION(Non-functional Binders)

NA.3: 5 residues within 4Å: Chain E: D.26, S.29, P.37, E.61, D.187 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.61 NA.4: 7 residues within 4Å: Chain E: D.26, D.30, G.186, H.189, Y.190, C.231, G.235 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:D.26 NA.11: 5 residues within 4Å: Chain L: D.26, S.29, S.35, E.61, D.187 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:E.61 NA.12: 7 residues within 4Å: Chain L: D.26, D.30, G.186, H.189, Y.190, C.231, G.235 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:D.26 NA.19: 5 residues within 4Å: Chain S: S.29, S.35, P.37, E.61, D.187 2 PLIP interactions: 2 interactions with chain S Hydrogen bonds: S:D.26, S:E.61 NA.20: 7 residues within 4Å: Chain S: D.26, D.30, G.186, H.189, Y.190, C.231, G.235 1 PLIP interactions: 1 interactions with chain S Hydrogen bonds: S:D.30

3 x COM: 1-THIOETHANESULFONIC ACID(Non-covalent)

COM.5: 10 residues within 4Å: Chain C: N.188 Chain E: S.35, N.36, N.38, S.39, Q.42, A.57, S.59, G.60, R.113 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.38 Salt bridges: E:R.113 COM.13: 10 residues within 4Å: Chain J: N.188 Chain L: Q.34, S.35, N.38, S.39, Q.42, A.57, S.59, G.60, R.113 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:N.38 Salt bridges: L:R.113 COM.21: 10 residues within 4Å: Chain Q: N.188, L.191 Chain R: A.29 Chain S: S.35, N.36, N.38, S.39, Q.42, A.57, R.113 2 PLIP interactions: 2 interactions with chain S Hydrogen bonds: S:N.38 Salt bridges: S:R.113

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Aziz, I. et al., Cryo-EM structure of the methanogenic Na+ translocating N5-methyl-H4MPT:CoM methyltransferase complex. To Be Published

Release Date

2024-08-21

Peptides

Tetrahydromethanopterin S-methyltransferase subunit A 1: AHO
Tetrahydromethanopterin S-methyltransferase subunit B: BIP
Tetrahydromethanopterin S-methyltransferase subunit C: CJQ
Tetrahydromethanopterin S-methyltransferase subunit D: DKR
Tetrahydromethanopterin S-methyltransferase subunit E: ELS
Tetrahydromethanopterin S-methyltransferase subunit F: FMT
Tetrahydromethanopterin S-methyltransferase subunit G: GNU

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

H
a

O
Q

B
B

I
b

P
R

C
C

J
c

Q
S

D
D

K
d

R
T

E
E

L
e

S
U

F
F

M
f

T
V

G
G

N
g

U
W

Membrane

We predict this structure to be a membrane protein.
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Tetrahydromethanopterin S-methyltransferase subunit A 1

Tetrahydromethanopterin S-methyltransferase subunit B

Tetrahydromethanopterin S-methyltransferase subunit C

Tetrahydromethanopterin S-methyltransferase subunit D

Tetrahydromethanopterin S-methyltransferase subunit E

Tetrahydromethanopterin S-methyltransferase subunit F

Tetrahydromethanopterin S-methyltransferase subunit G

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