SMTL ID : 2via.1

Crystal structure of S172AbsSHMT L-Serine external aldimine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.67 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 8 PLIP interactions: 2 interactions with chain B, 4 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 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 8 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: B:S.31, B:K.226, A:E.53, A:Y.61, S.6, S.6 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, A.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 13 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: A:A.199 Hydrogen bonds: A:G.94, A:A.95, B:E.53, B:G.256, B:G.257, S.1 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, A.172, D.197, A.199, H.200, T.223, H.225, K.226 Ligands: SER.6 13 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: B:A.199 Hydrogen bonds: B:G.94, B:A.95, A:E.53, A:G.256, A:G.257, S.6 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 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.152, A:I.186, 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 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.152, B:I.186, 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: 3 residues within 4Å: Chain A: E.371, E.372, E.375 No protein-ligand interaction detected (PLIP) PO4.10: 3 residues within 4Å: Chain B: E.371, E.372, E.375 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rajaram, V. et al., Crystal Structure of S172Absshmt and its Complexes. To be Published

Release Date

2007-12-18

Peptides

SERINE HYDROXYMETHYLTRANSFERASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

SERINE HYDROXYMETHYLTRANSFERASE

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