SMTL ID : 9hip.1

MnmE-MnmG a2b2 complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.31 Å

Oligo State

hetero-2-2-mer

Ligands

2 x GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER(Non-covalent)

GNP.1: 23 residues within 4Å: Chain A: R.224, P.225, N.226, A.227, G.228, K.229, S.230, S.231, V.244, T.245, D.246, T.250, T.251, D.270, T.271, A.272, G.273, N.335, K.336, D.338, I.339, A.359, R.360 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:N.226, A:A.227, A:G.228, A:K.229, A:K.229, A:S.230, A:S.231, A:S.231, A:T.245, A:T.250, A:T.250, A:T.251, A:T.271, A:G.273, A:K.336, A:K.336, A:A.359, A:R.360, A:R.360 pi-Cation interactions: A:R.360, A:R.360 GNP.2: 20 residues within 4Å: Chain B: P.225, N.226, A.227, G.228, K.229, S.230, S.231, V.244, T.245, D.246, I.247, T.250, T.251, G.273, N.335, K.336, D.338, I.339, A.359, R.360 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:N.226, B:G.228, B:G.228, B:K.229, B:K.229, B:S.230, B:S.231, B:T.245, B:T.245, B:I.247, B:T.250, B:T.250, B:T.251, B:G.273, B:N.335, B:K.336, B:K.336, B:A.359, B:R.360, B:R.360, B:R.360 Salt bridges: B:K.229, B:D.338

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.3: 30 residues within 4Å: Chain B: K.454 Chain C: I.32, G.33, G.34, G.35, H.36, A.37, L.55, T.56, H.57, S.66, C.67, Q.143, V.145, T.174, V.175, G.176, T.177, F.178, R.194, S.200, T.219, Y.361, I.363, G.389, Q.390, T.395, G.396, Y.397, A.400 22 PLIP interactions: 21 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:R.194, C:T.219, C:Y.361, C:I.363 Hydrogen bonds: C:G.34, C:H.36, C:A.37, C:H.57, C:H.57, C:V.145, C:V.145, C:S.200, C:T.219, C:Q.390, C:Q.390, C:T.395, C:T.395, C:G.396, B:K.454 Salt bridges: C:R.194 pi-Stacking: C:H.57, C:H.57

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maes, L. et al., Cryo-EM structures of the MnmE-MnmG complex reveal large conformational changes and provide new insights into the mechanism of tRNA modification. Nucleic Acids Res. (2025)

Release Date

2025-08-27

Peptides

tRNA modification GTPase MnmE: AB
tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

tRNA modification GTPase MnmE

tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG

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