SMTL ID : 6z81.1 (1 other biounit)

TsaBD bound to the inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

hetero-1-1-mer

Ligands

2 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 2 residues within 4Å: Chain A: H.339 Ligands: ACT.12 No protein-ligand interaction detected (PLIP) NI.2: 1 residues within 4Å: Chain A: L.321 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.111, H.115, D.300 Ligands: QCB.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.111, A:H.115, A:D.300

1 x QCB: (2~{S},3~{R})-2-[2-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]ethanoylamino]-3-oxidanyl-butanoic acid(Non-covalent)

QCB.4: 23 residues within 4Å: Chain A: S.9, C.10, P.82, G.83, H.111, M.112, H.115, S.136, G.137, G.138, H.139, G.163, F.166, D.167, G.180, P.181, G.268, V.269, A.271, N.272, T.299, D.300 Ligands: ZN.3 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:S.136, A:G.137, A:G.138, A:H.139, A:D.167, A:G.180, A:G.268, A:N.272, A:D.300, A:D.300 Water bridges: A:R.273, A:R.273 Salt bridges: A:H.111, A:H.115, A:H.139 pi-Stacking: A:F.166

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

SO4.5: 1 residues within 4Å: Chain A: R.237 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.237 SO4.6: 2 residues within 4Å: Chain A: K.168, K.171 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.168, A:K.171

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

NA.7: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.2 NA.13: 3 residues within 4Å: Chain B: S.52, L.53 Ligands: PEG.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.53

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

ACT.8: 7 residues within 4Å: Chain A: D.20, Y.307, M.310, V.311, K.314, H.340, H.341 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.20 Hydrogen bonds: A:H.341 Salt bridges: A:K.314 ACT.9: 3 residues within 4Å: Chain A: I.249, K.252, R.253 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.252, A:R.253 ACT.12: 3 residues within 4Å: Chain A: T.146, Q.150 Ligands: NI.1 No protein-ligand interaction detected (PLIP) ACT.15: 5 residues within 4Å: Chain B: P.215, V.216, Y.217, L.218, N.220 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.217, B:L.218, B:N.220, B:N.220 ACT.16: 8 residues within 4Å: Chain B: S.14, V.15, A.25, H.26, F.27, A.190, A.191, E.192 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:A.25, B:F.27, B:A.190, B:E.192 Hydrogen bonds: B:S.14, B:V.15, B:H.26, B:E.192 ACT.17: 4 residues within 4Å: Chain B: V.143, L.218, N.220, N.221 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:N.220 Hydrogen bonds: B:N.220, B:N.221

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.10: 4 residues within 4Å: Chain A: F.100, D.103 Chain B: Q.43 Ligands: NA.13 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:R.96, A:A.99 Hydrogen bonds: B:Q.43 PEG.11: 4 residues within 4Å: Chain A: Q.150, A.336, A.337, H.338 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.150, A:A.337, A:H.338

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.14: 9 residues within 4Å: Chain A: V.85, L.89 Chain B: R.32, E.33, H.34, T.35, S.67, T.69, I.73 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:C.30, B:R.32, B:H.34, B:H.34, B:S.67 Water bridges: B:T.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kopina, B.J. et al., Structure of a reaction intermediate mimic in t6A biosynthesis bound in the active site of the TsaBD heterodimer from Escherichia coli. Nucleic Acids Res. (2021)

Release Date

2021-02-10

Peptides

tRNA N6-adenosine threonylcarbamoyltransferase: A
tRNA threonylcarbamoyladenosine biosynthesis protein TsaB: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

tRNA N6-adenosine threonylcarbamoyltransferase

tRNA threonylcarbamoyladenosine biosynthesis protein TsaB

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