SMTL ID : 6nbj.1

Qri7

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.94 Å

Oligo State

homo-dimer

Ligands

1 x C- C- C- C: RNA (5'-R(P*CP*CP*CP*C)-3')(Non-covalent)

C-C-C-C.1: 15 residues within 4Å: Chain A: K.57, H.59, I.60, Q.63, M.94, P.95, G.96, S.97, S.99 Chain B: H.59, P.95, G.96, S.99, R.365 Ligands: ATP.5 Protein-ligand interaction information (PLIP) not available

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.121, H.125, H.151, D.337 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.121, A:H.125, A:H.151, A:D.337, H2O.1 ZN.6: 4 residues within 4Å: Chain B: H.121, H.125, H.151, D.337 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.121, B:H.125, B:H.151, B:D.337, H2O.1

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.3: 17 residues within 4Å: Chain A: S.148, G.149, G.175, D.179, M.191, I.192, A.193, R.194, E.197, G.300, G.301, V.302, S.304, N.305, M.332, C.335, S.336 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:G.149, A:D.179, A:A.193, A:R.194, A:R.194, A:E.197, A:E.197, A:G.301, A:S.304, A:N.305, A:C.335, A:S.336, A:D.337 Water bridges: A:S.148 AMP.7: 14 residues within 4Å: Chain B: S.148, G.149, D.179, A.193, R.194, E.197, G.300, G.301, V.302, S.304, N.305, M.332, C.335, S.336 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.149, B:D.179, B:A.193, B:R.194, B:E.197, B:E.197, B:G.301, B:N.305, B:C.335 Water bridges: B:S.148, B:S.148

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.4: 6 residues within 4Å: Chain A: K.7, Y.9, K.31, W.350, E.351, R.354 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.7, A:K.31, A:E.351

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.5: 8 residues within 4Å: Chain A: R.365 Chain B: K.57, H.59, M.94, P.95, G.96, S.97 Ligands: C-C-C-C.1 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.57, B:H.59, B:G.96, B:S.97, A:R.365, A:R.365 Salt bridges: B:K.57, B:K.57, B:H.59, B:H.59, B:H.59

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.8: 2 residues within 4Å: Chain B: K.180, R.241 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.180, B:R.241

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stec, B., Discovery of the Universal tRNA Binding Mode for the TsaD-like Components of the t6A tRNA Modification Pathway. Biophysica (2023)

Release Date

2023-04-26

Peptides

tRNA N6-adenosine threonylcarbamoyltransferase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

tRNA N6-adenosine threonylcarbamoyltransferase, mitochondrial

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