SMTL ID : 7xcn.1

Crystal structure of the MttB-MttC complex at 2.7 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-6-6-mer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: I.183, C.219, M.249, O.334, Y.364 Ligands: HCB.5 No protein-ligand interaction detected (PLIP) GOL.2: 7 residues within 4Å: Chain C: I.183, C.219, L.247, M.249, O.334, Y.364 Ligands: HCB.7 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.364 GOL.3: 7 residues within 4Å: Chain E: G.110, C.219, L.247, M.249, S.292, O.334 Ligands: HCB.9 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.292 GOL.4: 7 residues within 4Å: Chain F: I.183, C.219, L.247, M.249, O.334, Y.364 Ligands: HCB.10 No protein-ligand interaction detected (PLIP)

6 x HCB: 5-HYDROXYBENZIMIDAZOLYLCOBAMIDE(Non-covalent)

HCB.5: 42 residues within 4Å: Chain A: F.109, G.110, T.111, V.113, S.154, I.183, D.184, C.219, P.220, T.221, S.222, M.251, F.296, G.301, O.334, L.371, G.372, M.373 Chain G: G.104, D.105, I.106, H.107, S.108, I.109, G.110, I.113, V.114, A.150, S.151, S.152, L.154, M.155, T.156, M.181, G.183, G.184, A.185, G.201, S.203, A.204, A.207 Ligands: GOL.1 28 PLIP interactions: 16 interactions with chain G, 12 interactions with chain A, Hydrophobic interactions: G:I.113, G:V.114, G:L.154, G:L.154, G:A.207, A:T.221, A:F.296 Hydrogen bonds: G:G.104, G:I.106, G:S.108, G:I.109, G:G.110, G:S.151, G:S.151, G:L.154, G:T.156, G:A.204, A:T.111, A:T.111, A:S.154, A:I.183, A:C.219, A:S.222, A:L.371 Metal complexes: G:H.107 Water bridges: A:N.229, A:A.303, A:A.303 HCB.6: 44 residues within 4Å: Chain B: T.111, V.113, S.154, I.183, D.184, C.219, P.220, T.221, S.222, M.249, M.251, F.296, G.301, A.303, O.334, L.371, G.372, M.373 Chain E: M.441 Chain H: G.104, D.105, I.106, H.107, S.108, I.109, G.110, I.113, V.114, A.150, S.151, S.152, L.154, M.155, T.156, T.157, M.181, V.182, G.183, G.184, A.185, G.201, E.202, S.203, A.204 29 PLIP interactions: 18 interactions with chain H, 11 interactions with chain B, Hydrophobic interactions: H:I.106, H:I.113, H:V.114, H:L.154, H:L.154, B:V.113, B:T.221, B:M.249, B:F.296 Hydrogen bonds: H:D.105, H:I.106, H:H.107, H:S.108, H:I.109, H:S.151, H:S.151, H:T.156, H:T.156, H:T.157, H:G.184, H:A.204, B:T.111, B:T.111, B:S.154, B:I.183, B:D.184, B:C.219, B:S.222 Metal complexes: H:H.107 HCB.7: 42 residues within 4Å: Chain C: G.110, T.111, V.113, S.154, I.183, D.184, C.219, P.220, T.221, S.222, M.249, M.251, F.296, G.301, O.334, L.371, G.372 Chain D: M.441 Chain I: G.104, D.105, I.106, H.107, S.108, I.109, G.110, I.113, V.114, A.150, S.151, S.152, L.154, M.155, T.156, M.181, G.183, G.184, A.185, G.201, S.203, A.204, A.207 Ligands: GOL.2 27 PLIP interactions: 16 interactions with chain I, 11 interactions with chain C, Hydrophobic interactions: I:I.113, I:V.114, I:L.154, I:L.154, I:A.207, C:T.221, C:M.249, C:F.296 Hydrogen bonds: I:G.104, I:I.106, I:S.108, I:I.109, I:G.110, I:S.151, I:S.151, I:L.154, I:T.156, I:A.204, C:T.111, C:T.111, C:S.154, C:I.183, C:C.219, C:S.222, C:L.371 Metal complexes: I:H.107 Water bridges: C:T.111 HCB.8: 44 residues within 4Å: Chain D: F.109, G.110, T.111, V.113, S.154, I.183, D.184, C.219, P.220, T.221, S.222, M.249, M.251, F.296, G.301, A.303, O.334, L.371, G.372, M.373 Chain J: I.99, G.104, D.105, I.106, H.107, S.108, I.109, G.110, I.113, V.114, A.150, S.151, S.152, L.154, M.155, T.156, M.181, G.183, G.184, A.185, G.201, S.203, A.204, A.207 28 PLIP interactions: 16 interactions with chain J, 12 interactions with chain D, Hydrophobic interactions: J:I.113, J:V.114, J:L.154, J:L.154, J:A.207, D:T.221, D:F.296, D:A.303 Hydrogen bonds: J:G.104, J:I.106, J:S.108, J:I.109, J:S.151, J:S.151, J:L.154, J:T.156, J:A.185, J:A.204, D:T.111, D:T.111, D:S.154, D:I.183, D:C.219, D:S.222, D:L.371 Metal complexes: J:H.107 Water bridges: D:N.229, D:N.229 HCB.9: 41 residues within 4Å: Chain E: G.110, T.111, V.113, S.154, I.183, D.184, L.217, L.218, C.219, P.220, T.221, S.222, M.249, M.251, F.296, O.334, L.371, G.372 Chain K: D.105, I.106, H.107, I.109, G.110, I.113, V.114, A.150, S.151, S.152, L.154, M.155, T.156, M.181, G.183, G.184, A.185, G.201, E.202, S.203, A.204, A.207 Ligands: GOL.3 29 PLIP interactions: 12 interactions with chain E, 17 interactions with chain K, Hydrophobic interactions: E:T.221, E:M.249, K:I.109, K:I.113, K:V.114, K:V.114, K:A.207 Hydrogen bonds: E:T.111, E:T.111, E:S.154, E:I.183, E:D.184, E:C.219, E:S.222, E:L.371, K:D.105, K:I.106, K:H.107, K:I.109, K:V.114, K:S.151, K:S.151, K:T.156, K:T.156 Water bridges: E:N.229, E:N.229, K:G.110, K:G.110 Metal complexes: K:H.107 HCB.10: 41 residues within 4Å: Chain F: G.110, T.111, V.113, S.154, I.183, D.184, C.219, P.220, T.221, S.222, M.249, M.251, F.296, G.301, O.334, L.371, G.372 Chain L: G.104, D.105, I.106, H.107, S.108, I.109, G.110, I.113, V.114, A.150, S.151, S.152, L.154, M.155, T.156, M.181, G.183, G.184, A.185, G.201, S.203, A.204, A.207 Ligands: GOL.4 26 PLIP interactions: 16 interactions with chain L, 10 interactions with chain F, Hydrophobic interactions: L:I.113, L:V.114, L:L.154, L:L.154, L:A.207, F:T.221, F:M.249, F:F.296 Hydrogen bonds: L:G.104, L:I.106, L:S.108, L:I.109, L:G.110, L:S.151, L:S.151, L:L.154, L:T.156, L:A.204, F:T.111, F:T.111, F:S.154, F:I.183, F:C.219, F:S.222, F:L.371 Metal complexes: L:H.107

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, J. et al., Insights into pyrrolysine function from structures of a trimethylamine methyltransferase and its corrinoid protein complex. Commun Biol (2023)

Release Date

2023-01-18

Peptides

Trimethylamine methyltransferase: ABCDEF
Trimethylamine methyltransferase corrinoid protein: GHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
M

H
N

I
O

J
P

K
Q

L
R

Trimethylamine methyltransferase

Trimethylamine methyltransferase corrinoid protein

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