SMTL ID : 6nak.1

BACTERIAL PROTEIN COMPLEX TM BDE complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.14 Å

Oligo State

hetero-2-2-2-mer

Ligands

2 x TXA: threonylcarbamoyladenylate(Non-covalent)

TXA.1: 21 residues within 4Å: Chain B: H.113, M.132, S.134, G.135, G.136, H.137, G.161, F.164, D.165, G.178, P.179, D.182, G.263, G.264, V.265, A.267, N.268, L.293, T.295 Chain C: F.87 Ligands: ZN.2 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:S.134, B:G.135, B:G.136, B:D.165, B:G.178, B:D.182, B:D.182, B:G.264, B:N.268, B:T.295, B:T.295 Salt bridges: B:H.113, B:H.137 pi-Stacking: B:F.164 TXA.5: 19 residues within 4Å: Chain E: H.113, M.132, S.134, G.135, G.136, H.137, G.161, F.164, D.165, G.178, P.179, D.182, G.263, G.264, V.265, A.267, N.268 Chain F: F.87 Ligands: ZN.6 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:S.134, E:G.135, E:G.136, E:D.165, E:G.178, E:D.182, E:D.182, E:G.264, E:N.268 Salt bridges: E:H.113, E:H.137 pi-Stacking: E:F.164

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain B: H.109, H.113, T.295 Ligands: TXA.1 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.109 ZN.6: 4 residues within 4Å: Chain E: H.109, H.113, D.296 Ligands: TXA.5 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:H.113

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain C: T.65, S.84, D.103, E.131 Ligands: APC.4 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.65, C:E.131 MG.7: 5 residues within 4Å: Chain F: T.65, S.84, D.103, E.131 Ligands: APC.8 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:T.65, F:E.131

2 x APC: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER(Non-covalent)

APC.4: 23 residues within 4Å: Chain B: K.166, A.210, K.213, T.214 Chain C: L.32, T.33, E.34, L.37, L.60, G.61, A.62, G.63, K.64, T.65, T.66, D.103, E.131, W.132, E.154, S.155, H.156, R.157 Ligands: MG.3 16 PLIP interactions: 13 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:E.34, C:G.61, C:G.63, C:K.64, C:T.65, C:T.65, C:T.66, C:T.66, C:S.155, C:R.157, B:K.213 Salt bridges: C:K.64, B:K.166, B:K.213 pi-Cation interactions: C:R.157, C:R.157 APC.8: 22 residues within 4Å: Chain E: K.166, A.210, G.211, K.213, T.214 Chain F: L.32, T.33, E.34, L.37, N.59, L.60, G.61, G.63, K.64, T.65, T.66, E.131, W.132, S.155, H.156, R.157 Ligands: MG.7 19 PLIP interactions: 15 interactions with chain F, 4 interactions with chain E Hydrogen bonds: F:E.34, F:G.61, F:G.63, F:K.64, F:K.64, F:T.65, F:T.65, F:T.66, F:T.66, F:D.103, F:S.155, F:R.157, E:A.210, E:K.213 Salt bridges: F:K.64, E:K.166, E:K.213 pi-Cation interactions: F:R.157, F:R.157

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 threonylcarbamoyladenosine biosynthesis protein TsaB: AD
tRNA N6-adenosine threonylcarbamoyltransferase: BE
TsaE: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
C

B
B

E
G

C
D

F
E

tRNA threonylcarbamoyladenosine biosynthesis protein TsaB

tRNA N6-adenosine threonylcarbamoyltransferase

TsaE

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