SMTL ID : 8sf6.3 (2 other biounits)

Promiscuous amino acid gamma synthase from Caldicellulosiruptor hydrothermalis in closed conformation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

4 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.1: 13 residues within 4Å: Chain A: Y.112, N.159, K.209, A.367, N.368, V.369, T.383, R.403 Chain B: F.48, Y.57, R.59, I.60, R.268 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.268, A:N.159 Water bridges: B:R.59 Salt bridges: A:R.403 MES.6: 13 residues within 4Å: Chain A: F.48, Y.57, R.59, I.60, R.268 Chain B: Y.112, N.159, K.209, A.367, N.368, V.369, T.383, R.403 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.268, B:Y.112, B:N.159 Water bridges: A:R.59 Salt bridges: B:R.403 MES.9: 13 residues within 4Å: Chain C: Y.112, N.159, K.209, A.367, N.368, V.369, T.383, R.403 Chain D: F.48, Y.57, R.59, I.60, R.268 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Y.112, C:N.159, D:R.268 Salt bridges: C:R.403 Water bridges: D:R.59 MES.14: 13 residues within 4Å: Chain C: F.48, Y.57, R.59, I.60, R.268 Chain D: Y.112, N.159, K.209, A.367, N.368, V.369, T.383, R.403 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:R.268, D:N.159 Water bridges: C:R.59 Salt bridges: D:R.403

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

NA.2: 4 residues within 4Å: Chain A: N.358 Chain B: E.39, T.40 Ligands: NA.4 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.39 NA.3: 3 residues within 4Å: Chain A: E.39, T.40 Chain B: N.358 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.39 NA.4: 2 residues within 4Å: Chain A: N.358 Ligands: NA.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.358 NA.5: 2 residues within 4Å: Chain A: H.310, V.313 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.313 NA.10: 4 residues within 4Å: Chain C: N.358 Chain D: E.39, T.40 Ligands: NA.12 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.358, C:N.358 NA.11: 3 residues within 4Å: Chain C: E.39, T.40 Chain D: N.358 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.358 NA.12: 2 residues within 4Å: Chain C: N.358 Ligands: NA.10 1 PLIP interactions: 1 interactions with chain D Water bridges: D:E.39 NA.13: 2 residues within 4Å: Chain C: H.310, V.313 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.308

2 x ETE: 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL(Non-covalent)

ETE.7: 6 residues within 4Å: Chain B: G.226, K.227, E.252, F.253, G.254, N.255 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.255, B:N.255 Water bridges: B:F.228 ETE.15: 6 residues within 4Å: Chain D: G.226, K.227, E.252, F.253, G.254, N.255 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.255, D:N.255 Water bridges: D:F.228

2 x AE3: 2-(2-ETHOXYETHOXY)ETHANOL(Non-covalent)

AE3.8: 5 residues within 4Å: Chain B: L.50, E.252, F.253, A.260, R.263 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.253 Water bridges: B:R.263 AE3.16: 5 residues within 4Å: Chain D: L.50, E.252, F.253, A.260, R.263 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.253 Water bridges: D:R.263

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zmich, A. et al., Multiplexed Assessment of Promiscuous Non-Canonical Amino Acid Synthase Activity in a Pyridoxal Phosphate-Dependent Protein Family. Acs Catalysis (2023)

Release Date

2023-12-27

Peptides

O-acetylhomoserine/O-acetylserine sulfhydrylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
E

C
C

D
E

O-acetylhomoserine/O-acetylserine sulfhydrylase

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