SMTL ID : 6uld.1

Crystal structure of serine hydroxymethyltransferase from Mycobacterium tuberculosis with bound PLP forming a Schiff base with substrate Serine in one monomer and PLP forming a Schiff base with product Glycine in the other monomer

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PLP.1: 18 residues within 4Å: Chain A: S.115, G.116, A.117, N.120, H.144, W.193, S.194, D.219, A.221, H.222, T.245, H.247, K.248 Chain B: Y.73, E.75, G.278, G.279 Ligands: GLY.2 18 PLIP interactions: 11 interactions with chain A, 4 interactions with chain B, 3 Ligand-Ligand interactions Hydrophobic interactions: A:A.221 Hydrogen bonds: A:S.115, A:G.116, A:A.117, A:N.120, A:S.194, B:Y.73, B:E.75, B:G.278, B:G.279, G.2 Water bridges: A:S.115, A:S.115, G.2, G.2 Salt bridges: A:H.247, A:K.248 pi-Stacking: A:H.144 PLP.4: 17 residues within 4Å: Chain A: Y.73, G.278, G.279 Chain B: S.115, G.116, A.117, N.120, H.144, W.193, S.194, D.219, A.221, H.222, T.245, H.247, K.248 Ligands: SER.3 14 PLIP interactions: 10 interactions with chain B, 3 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: B:A.221 Hydrogen bonds: B:S.115, B:G.116, B:A.117, B:N.120, B:H.222, A:Y.73, A:G.278, A:G.279, S.3 Water bridges: B:S.115, B:S.115 Salt bridges: B:H.247 pi-Stacking: B:H.144

1 x GLY: GLYCINE(Non-covalent)

GLY.2: 9 residues within 4Å: Chain A: S.53, H.144, S.194, H.222, K.248, R.384 Chain B: Y.73, Y.83 Ligands: PLP.1 9 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: A:S.53, A:H.144, A:S.194, A:S.194, B:Y.83, G.2 Salt bridges: A:H.222, A:K.248, A:R.384

1 x SER: SERINE(Non-covalent)

SER.3: 10 residues within 4Å: Chain A: Y.73, E.75, Y.83 Chain B: S.53, H.144, S.194, H.222, K.248, R.384 Ligands: PLP.4 13 PLIP interactions: 8 interactions with chain B, 3 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: B:S.53, B:H.144, B:S.194, B:S.194, B:K.248, A:E.75, A:Y.83, S.3, S.3 Salt bridges: B:H.222, B:K.248, B:R.384 Water bridges: A:E.75

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.5: 5 residues within 4Å: Chain B: G.131, K.156, L.157, Y.158, E.159 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.131, B:K.156 MPD.6: 8 residues within 4Å: Chain B: G.76, L.77, R.80, Y.82, N.269, S.270, F.273, P.274 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.77, B:L.77, B:R.80, B:Y.82, B:N.269, B:F.273 Hydrogen bonds: B:Y.82, B:F.273

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dranow, D.M. et al., Crystal structure of serine hydroxymethyltransferase from Mycobacterium tuberculosis with bound PLP forming a Schiff base with substrate Serine in one monomer and PLP forming a Schiff base with product Glycine in the other monomer. to be published

Release Date

2019-10-16

Peptides

Serine hydroxymethyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Serine hydroxymethyltransferase

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