SMTL ID : 4m3p.1

Betaine-Homocysteine S-Methyltransferase from Homo sapiens complexed with Homocysteine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.217, C.299, C.300 Ligands: HCS.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.217, A:C.299, A:C.300 ZN.5: 4 residues within 4Å: Chain B: C.217, C.299, C.300 Ligands: HCS.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.217, B:C.299, B:C.300 ZN.8: 6 residues within 4Å: Chain C: N.216, C.217, L.249, C.299, C.300 Ligands: HCS.10 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.217, C:C.299, C:C.300 ZN.12: 4 residues within 4Å: Chain D: C.217, C.299, C.300 Ligands: HCS.14 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.217, D:C.299, D:C.300

4 x K: POTASSIUM ION(Non-covalent)

K.2: 6 residues within 4Å: Chain A: D.26, G.27, Q.72, Q.247, G.298, C.299 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.26, A:D.26, A:G.298, H2O.1, H2O.6 K.6: 6 residues within 4Å: Chain B: D.26, G.27, Q.72, Q.247, G.298, C.299 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.26, B:D.26, B:G.298, H2O.11, H2O.12 K.9: 6 residues within 4Å: Chain C: D.26, G.27, Q.72, Q.247, G.298, C.299 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.26, C:D.26, C:G.298, H2O.14, H2O.15 K.13: 6 residues within 4Å: Chain D: D.26, G.27, Q.72, Q.247, G.298, C.299 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.26, D:D.26, D:G.27, D:G.298

4 x HCS: 2-AMINO-4-MERCAPTO-BUTYRIC ACID(Non-covalent)

HCS.3: 12 residues within 4Å: Chain A: G.27, G.28, F.29, V.30, Q.72, E.159, Y.160, N.216, C.217, C.299, C.300 Ligands: ZN.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.29, A:V.30, A:Q.72, A:E.159 HCS.7: 12 residues within 4Å: Chain B: G.27, G.28, F.29, V.30, Q.72, E.159, Y.160, N.216, C.217, C.299, C.300 Ligands: ZN.5 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:F.29, B:V.30, B:Q.72, B:E.159 Water bridges: B:F.31 HCS.10: 12 residues within 4Å: Chain C: G.27, G.28, F.29, V.30, Q.72, E.159, Y.160, N.216, C.217, C.299, C.300 Ligands: ZN.8 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:F.29, C:V.30, C:E.159 Water bridges: C:G.27, C:Q.72, C:G.298 HCS.14: 12 residues within 4Å: Chain D: G.27, G.28, F.29, V.30, Q.72, E.159, Y.160, N.216, C.217, C.299, C.300 Ligands: ZN.12 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:F.29, D:V.30, D:E.159 Water bridges: D:G.27, D:F.31

2 x SRT: S,R MESO-TARTARIC ACID(Non-covalent)

SRT.4: 5 residues within 4Å: Chain A: E.54, R.57 Chain B: E.54, R.57, R.61 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.57, B:R.61, B:R.61 Salt bridges: B:R.57 SRT.11: 5 residues within 4Å: Chain C: E.54, R.57 Chain D: E.54, R.57, R.61 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:R.61, D:R.61, C:R.57 Salt bridges: D:R.57

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mladkova, J. et al., Specific potassium ion interactions facilitate homocysteine binding to betaine-homocysteine S-methyltransferase. Proteins (2014)

Release Date

2014-06-18

Peptides

Betaine--homocysteine S-methyltransferase 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Betaine--homocysteine S-methyltransferase 1