SMTL ID : 1lt8.1

Reduced Homo sapiens Betaine-Homocysteine S-Methyltransferase in Complex with S-(delta-carboxybutyl)-L-Homocysteine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 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: CBH.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.217, A:C.299, A:C.300 ZN.4: 4 residues within 4Å: Chain B: C.217, C.299, C.300 Ligands: CBH.5 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.217, B:C.299, B:C.300 ZN.7: 4 residues within 4Å: Chain C: C.217, C.299, C.300 Ligands: CBH.8 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.217, C:C.299, C:C.300 ZN.10: 4 residues within 4Å: Chain D: C.217, C.299, C.300 Ligands: CBH.11 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.217, D:C.299, D:C.300

4 x CBH: S-(D-CARBOXYBUTYL)-L-HOMOCYSTEINE(Non-covalent)

CBH.2: 17 residues within 4Å: Chain A: G.27, G.28, F.29, V.30, W.44, Q.72, F.76, Y.77, E.159, Y.160, C.217, I.262, F.267, C.299, C.300 Chain B: H.338 Ligands: ZN.1 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.76, A:F.76, A:Y.160, A:I.262 Hydrogen bonds: A:F.29, A:V.30, A:Y.77, A:E.159 Water bridges: A:G.27, A:F.31, A:Q.72 Salt bridges: B:H.338 CBH.5: 16 residues within 4Å: Chain A: H.338 Chain B: G.27, G.28, F.29, V.30, W.44, Q.72, F.76, Y.77, E.159, Y.160, C.217, F.267, C.299, C.300 Ligands: ZN.4 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.76, B:F.76, B:Y.160 Hydrogen bonds: B:F.29, B:V.30, B:Q.72, B:E.159 Water bridges: B:Q.72, B:E.159 Salt bridges: A:H.338 CBH.8: 17 residues within 4Å: Chain C: G.27, G.28, F.29, V.30, W.44, Q.72, F.76, Y.77, E.159, Y.160, C.217, I.262, F.267, C.299, C.300 Chain D: H.338 Ligands: ZN.7 12 PLIP interactions: 10 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:F.76, C:F.76, C:Y.160, C:I.262 Hydrogen bonds: C:F.29, C:V.30, C:E.159 Water bridges: C:G.27, C:F.31, C:Q.72, D:H.338 Salt bridges: D:H.338 CBH.11: 16 residues within 4Å: Chain C: H.338 Chain D: G.27, G.28, F.29, V.30, W.44, Q.72, F.76, Y.77, E.159, Y.160, C.217, F.267, C.299, C.300 Ligands: ZN.10 11 PLIP interactions: 10 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:F.76, D:F.76, D:Y.160 Hydrogen bonds: D:F.29, D:V.30, D:Q.72, D:Y.77, D:E.159 Water bridges: D:Q.72, D:E.159 Salt bridges: C:H.338

4 x CIT: CITRIC ACID(Non-functional Binders)

CIT.3: 8 residues within 4Å: Chain A: D.220, H.252, P.254, R.356 Chain B: G.360, P.362, Y.363 Chain D: K.369 9 PLIP interactions: 6 interactions with chain A, 1 interactions with chain D, 2 interactions with chain B Hydrogen bonds: A:H.252 Water bridges: A:T.222, A:R.356, B:N.364 Salt bridges: A:H.252, A:H.252, A:R.356, D:K.369 Hydrophobic interactions: B:Y.363 CIT.6: 9 residues within 4Å: Chain A: G.360, P.362, Y.363, N.364 Chain B: D.220, H.252, P.254, R.356 Chain C: K.369 8 PLIP interactions: 6 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Water bridges: B:T.222, B:T.222, B:R.356, B:R.356 Salt bridges: B:H.252, B:R.356, C:K.369 Hydrophobic interactions: A:Y.363 CIT.9: 8 residues within 4Å: Chain B: K.369 Chain C: D.220, H.252, P.254, R.356 Chain D: G.360, P.362, Y.363 9 PLIP interactions: 6 interactions with chain C, 2 interactions with chain D, 1 interactions with chain B Water bridges: C:T.222, C:T.222, C:R.356, D:N.364 Salt bridges: C:H.252, C:H.252, C:R.356, B:K.369 Hydrophobic interactions: D:Y.363 CIT.12: 9 residues within 4Å: Chain A: K.369 Chain C: G.360, P.362, Y.363, N.364 Chain D: D.220, H.252, P.254, R.356 8 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 6 interactions with chain D Hydrophobic interactions: C:Y.363 Salt bridges: A:K.369, D:H.252, D:R.356 Water bridges: D:T.222, D:T.222, D:R.356, D:R.356

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Evans, J.C. et al., Betaine-homocysteine methyltransferase: zinc in a distorted barrel. Structure (2002)

Release Date

2002-09-11

Peptides

BETAINE-HOMOCYSTEINE METHYLTRANSFERASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

BETAINE-HOMOCYSTEINE METHYLTRANSFERASE

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