SMTL ID : 2vmw.1

Crystal structure of F351GbsSHMT in complex with L-Ser

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

homo-dimer

Ligands

2 x SER: SERINE(Non-covalent)

SER.1: 9 residues within 4Å: Chain A: S.31, H.122, H.200, K.226, R.357 Chain B: Y.51, E.53, Y.61 Ligands: PLP.2 9 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: B:E.53, B:Y.61, A:S.31, A:K.226, S.1, S.1 Water bridges: A:S.172 Salt bridges: A:H.200, A:R.357 SER.6: 9 residues within 4Å: Chain A: Y.51, E.53, Y.61 Chain B: S.31, H.122, H.200, K.226, R.357 Ligands: PLP.7 9 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B, 2 Ligand-Ligand interactions Hydrogen bonds: A:E.53, A:Y.61, B:S.31, B:K.226, S.6, S.6 Water bridges: B:S.172 Salt bridges: B:H.200, B:R.357

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

PLP.2: 17 residues within 4Å: Chain A: S.93, G.94, A.95, H.122, A.171, S.172, D.197, A.199, H.200, T.223, H.225, K.226 Chain B: Y.51, E.53, G.256, G.257 Ligands: SER.1 15 PLIP interactions: 3 interactions with chain B, 11 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: B:E.53, B:G.256, B:G.257, A:G.94, A:A.95, A:N.98, A:S.172, S.1 Hydrophobic interactions: A:A.199 Water bridges: A:S.93, A:S.93, A:T.221 Salt bridges: A:H.225, A:K.226 pi-Stacking: A:H.122 PLP.7: 17 residues within 4Å: Chain A: Y.51, E.53, G.256, G.257 Chain B: S.93, G.94, A.95, H.122, A.171, S.172, D.197, A.199, H.200, T.223, H.225, K.226 Ligands: SER.6 15 PLIP interactions: 3 interactions with chain A, 11 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: A:E.53, A:G.256, A:G.257, B:G.94, B:A.95, B:N.98, B:S.172, S.6 Hydrophobic interactions: B:A.199 Water bridges: B:S.93, B:S.93, B:T.221 Salt bridges: B:H.225, B:K.226 pi-Stacking: B:H.122

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

MPD.3: 5 residues within 4Å: Chain A: Y.152, D.153, R.156, E.185, I.186 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.152, A:I.186 Water bridges: A:K.182 MPD.4: 9 residues within 4Å: Chain A: M.99, F.103, F.131, Q.135, Y.136, I.254 Chain B: F.103, I.254 Ligands: MPD.9 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.103, B:I.254, A:F.103, A:F.131 MPD.8: 5 residues within 4Å: Chain B: Y.152, D.153, R.156, E.185, I.186 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.152, B:I.186 Water bridges: B:K.182 MPD.9: 9 residues within 4Å: Chain A: F.103, I.254 Chain B: M.99, F.103, F.131, Q.135, Y.136, I.254 Ligands: MPD.4 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.103, B:F.131, A:F.103, A:I.254

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 4 residues within 4Å: Chain A: E.371, E.372, E.375, L.403 No protein-ligand interaction detected (PLIP) PO4.10: 4 residues within 4Å: Chain B: E.371, E.372, E.375, L.403 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pai, V.R. et al., Structural and Functional Studies of Bacillus Stearothermophilus Serine Hydroxymethyltransferase: The Role of N341, Y60 and F351 in Tetrahydrofolate Binding. Biochem.J. (2009)

Release Date

2008-12-16

Peptides

SERINE HYDROXYMETHYLTRANSFERASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

SERINE HYDROXYMETHYLTRANSFERASE

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