SMTL ID : 8ap0.1

ForT Mutant T138V

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x PRP: 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose(Non-covalent)

PRP.1: 17 residues within 4Å: Chain A: R.19, Q.98, H.99, S.100, G.101, F.102, G.103, S.104, K.105, T.106, S.139, A.141, S.142, S.174, V.294 Ligands: MYO.2, MG.6 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:H.99, A:G.101, A:G.103, A:S.104, A:S.104, A:K.105, A:T.106, A:T.106, A:S.139, A:S.139, A:A.141, A:S.142, A:S.142 Water bridges: A:S.100, A:S.100, A:T.106, A:R.135, A:R.135, A:R.135, A:T.143, A:S.293 Salt bridges: A:R.19, A:R.19, A:R.19, A:H.99 PRP.7: 17 residues within 4Å: Chain B: R.19, Q.98, H.99, S.100, G.101, F.102, G.103, S.104, K.105, T.106, S.139, A.141, S.142, S.174, V.294 Ligands: MYO.8, MG.12 26 PLIP interactions: 26 interactions with chain B Hydrogen bonds: B:H.99, B:G.101, B:G.103, B:S.104, B:S.104, B:K.105, B:T.106, B:S.139, B:S.139, B:A.141, B:S.142, B:S.142 Water bridges: B:H.99, B:H.99, B:S.100, B:S.100, B:T.106, B:R.135, B:R.135, B:R.135, B:T.143, B:S.293 Salt bridges: B:R.19, B:R.19, B:R.19, B:H.99

2 x MYO: 4-azanyl-1~{H}-pyrazole-3,5-dicarboxylic acid(Non-covalent)

MYO.2: 10 residues within 4Å: Chain A: S.21, L.24, I.37, V.138, S.139, P.173, S.174, Q.266, V.294 Ligands: PRP.1 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.21, A:S.174, A:Q.266, A:Q.266 Water bridges: A:L.24, A:S.139, A:E.211, A:E.211, A:V.294, A:V.294 Salt bridges: A:K.263 MYO.8: 10 residues within 4Å: Chain B: S.21, L.24, I.37, V.138, S.139, P.173, S.174, Q.266, V.294 Ligands: PRP.7 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:S.21, B:S.174, B:Q.266, B:Q.266 Water bridges: B:L.24, B:S.139, B:E.211, B:E.211, B:E.211, B:E.211, B:V.294, B:V.294 Salt bridges: B:K.263

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: W.194, P.195, F.246, T.303, K.304 3 PLIP interactions: 3 interactions with chain A Water bridges: A:T.303, A:T.303, A:K.304 GOL.4: 7 residues within 4Å: Chain A: S.30, S.31, W.227 Chain B: R.228, H.231, L.232, E.255 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.228, B:H.231, B:E.255, B:E.255 Water bridges: A:S.30 GOL.9: 5 residues within 4Å: Chain B: W.194, P.195, F.246, T.303, K.304 3 PLIP interactions: 3 interactions with chain B Water bridges: B:T.303, B:T.303, B:K.304 GOL.10: 7 residues within 4Å: Chain A: R.228, H.231, L.232, E.255 Chain B: S.30, S.31, W.227 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.228, A:H.231, A:E.255 Water bridges: B:S.30

2 x K: POTASSIUM ION(Non-covalent)

K.5: 4 residues within 4Å: Chain A: G.281, R.282, A.284, V.287 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.281, A:R.282, A:V.287, H2O.9, H2O.10 K.11: 4 residues within 4Å: Chain B: G.281, R.282, A.284, V.287 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:G.281, B:R.282, B:V.287, H2O.21, H2O.22

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 2 residues within 4Å: Chain A: H.99 Ligands: PRP.1 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain B: H.99 Ligands: PRP.7 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, W. et al., Experimental and computational snapshots of C-C bond formation in a C-nucleoside synthase. Open Biology (2023)

Release Date

2022-09-07

Peptides

Beta-ribofuranosylaminobenzene 5'-phosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
AAA

Beta-ribofuranosylaminobenzene 5'-phosphate synthase