SMTL ID : 9k05.1

Crystal structure of Pyrococcus abyssi AIR synthetase N186A mutant bound to FGAR and AMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x FGR: N-(N-FORMYLGLYCYL)-5-O-PHOSPHONO-BETA-D-RIBOFURANOSYLAMINE(Non-covalent)

FGR.1: 17 residues within 4Å: Chain A: Y.4, V.9, D.61, G.62, G.64, T.65, M.86, S.185, A.186, G.187, L.188, T.189 Chain B: E.137, T.138, A.139, V.140, M.141 18 PLIP interactions: 2 interactions with chain B, 16 interactions with chain A Hydrogen bonds: B:V.140, A:Y.4, A:Y.4, A:G.62, A:G.62, A:T.65, A:G.187, A:L.188, A:T.189 Water bridges: B:T.138, A:E.11, A:E.11, A:E.11, A:E.11, A:V.63, A:K.66, A:S.185, A:G.242 FGR.4: 17 residues within 4Å: Chain A: E.137, T.138, A.139, V.140, M.141 Chain B: Y.4, V.9, D.61, G.62, G.64, T.65, M.86, S.185, A.186, G.187, L.188, T.189 21 PLIP interactions: 19 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Y.4, B:Y.4, B:G.62, B:G.62, B:T.65, B:G.187, B:L.188, B:T.189, B:T.189, B:T.189, A:V.140 Water bridges: B:E.11, B:E.11, B:E.11, B:E.11, B:E.11, B:V.63, B:K.66, B:T.241, B:G.242, A:T.138

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.2: 11 residues within 4Å: Chain A: D.103, G.135, G.136, E.137, T.138 Chain B: L.18, I.21, I.22, G.43, H.44, R.250 20 PLIP interactions: 9 interactions with chain A, 11 interactions with chain B Hydrogen bonds: A:G.136, A:E.137, A:E.137, A:T.138, A:T.138, B:G.43, B:G.43 Water bridges: A:G.136, A:E.137, A:E.137, A:T.138, B:H.44, B:H.44, B:H.44, B:Y.45, B:R.250, B:R.250, B:R.250, B:R.250 Salt bridges: B:R.250 AMP.3: 11 residues within 4Å: Chain A: L.18, I.21, I.42, G.43, H.44, R.250 Chain B: D.103, G.135, G.136, E.137, T.138 18 PLIP interactions: 8 interactions with chain A, 10 interactions with chain B Hydrogen bonds: A:G.43, A:G.43, B:G.136, B:E.137, B:E.137, B:T.138 Water bridges: A:H.44, A:T.60, A:R.250, A:R.250, A:R.250, B:G.136, B:G.136, B:E.137, B:E.137, B:T.138, B:T.138 Salt bridges: A:R.250

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, Y.H. et al., Crystal structure of Pyrococcus abyssi AIR synthetase N186A mutant bound to FGAR and AMP. To Be Published

Release Date

2025-10-15

Peptides

Phosphoribosylformylglycinamidine cyclo-ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Phosphoribosylformylglycinamidine cyclo-ligase