SMTL ID : 8cp3.1

Apo-LarE in complex with AMP-PNP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 18 residues within 4Å: Chain A: A.38, Y.39, S.40, G.42, V.43, D.44, S.45, V.61, T.62, I.63, F.68, K.111, I.114, D.132, G.133, T.134, R.143, F.149 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:S.40, A:S.40, A:G.42, A:D.44, A:D.44, A:S.45, A:I.63, A:I.63, A:G.133, A:G.133, A:G.133, A:R.143 Water bridges: A:V.43 Salt bridges: A:K.111, A:R.143 ANP.5: 19 residues within 4Å: Chain B: A.38, Y.39, S.40, G.42, V.43, D.44, S.45, V.61, T.62, I.63, F.68, K.111, I.114, D.132, G.133, T.134, R.143, F.149 Ligands: SO4.9 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:S.40, B:G.42, B:G.42, B:D.44, B:D.44, B:D.44, B:S.45, B:I.63, B:I.63, B:G.133, B:G.133, B:R.143 Salt bridges: B:K.111

2 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.2: 5 residues within 4Å: Chain A: N.65, F.67, C.110, K.111, I.114 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.65 BME.7: 7 residues within 4Å: Chain A: T.184, C.185 Chain B: N.65, F.67, C.110, K.111, I.114 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.184

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

SO4.3: 4 residues within 4Å: Chain A: S.40, G.42, F.68, V.72 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.40 SO4.4: 4 residues within 4Å: Chain A: S.53, D.54, N.55, A.56 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.56 SO4.8: 4 residues within 4Å: Chain A: R.221, R.223 Chain B: R.143, K.165 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.143 Salt bridges: B:K.165, A:R.221, A:R.223 SO4.9: 3 residues within 4Å: Chain B: G.42, V.43 Ligands: ANP.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.43 SO4.10: 4 residues within 4Å: Chain B: R.79, K.82, D.178, P.180 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.79, B:K.82 SO4.11: 1 residues within 4Å: Chain B: K.34 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.34

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 6 residues within 4Å: Chain B: P.11, M.12, I.13, L.20, N.24, L.27 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:M.12, B:I.13, B:I.13, B:N.24, B:N.24

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zecchin, P. et al., Structure-based insights into the mechanism of [4Fe-4S]-dependent sulfur insertase LarE. Protein Sci. (2024)

Release Date

2024-01-31

Peptides

NAD_synthase domain-containing protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NAD_synthase domain-containing protein

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