SMTL ID : 8sui.1

Joint X-ray/neutron structure of Thermus thermophilus serine hydroxymethyltransferase (TthSHMT) in internal aldimine state with L-Ser bound in a pre-Michalis complex

Coordinates

PDB Format Compare

Method

NEUTRON DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 8 residues within 4Å: Chain A: S.29, H.120, S.170, H.198, K.224, R.356 Chain B: Y.59 Ligands: SER.3 8 PLIP interactions: 6 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:S.29, A:S.170 Water bridges: A:H.120, A:H.120, S.3, S.3 Salt bridges: A:H.198, A:R.356 SO4.2: 8 residues within 4Å: Chain A: Y.49, Y.59 Chain B: S.29, H.120, S.170, H.198, K.224, R.356 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.29, A:Y.49, A:Y.59 Water bridges: B:H.120, B:H.120, B:H.120, B:H.120 Salt bridges: B:H.198, B:R.356

1 x SER: SERINE(Non-covalent)

SER.3: 7 residues within 4Å: Chain A: L.115, L.121, N.338 Chain B: E.51, Y.58, Y.59 Ligands: SO4.1 10 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B, 4 Ligand-Ligand interactions Water bridges: A:H.120, A:K.339, A:K.339, B:E.51, S.3, S.3 Salt bridges: A:K.339 Hydrogen bonds: B:Y.59, S.3, S.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Drago, V.N. et al., Revealing protonation states and tracking substrate in serine hydroxymethyltransferase with room-temperature X-ray and neutron crystallography. Commun Chem (2023)

Release Date

2023-08-16

Peptides

Serine hydroxymethyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Serine hydroxymethyltransferase

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