SMTL ID : 6sw5.1 (1 other biounit)

Crystal structure of the human S-adenosylmethionine synthetase 1 (ligand-free form)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.1: 7 residues within 4Å: Chain A: Q.317, F.333 Chain B: F.18, W.274, R.313, Y.335 Ligands: PEG.8 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.313, B:R.313, A:Q.317 PEG.8: 8 residues within 4Å: Chain A: A.276, L.315, Y.335 Chain B: G.273, G.275, Y.335 Ligands: PEG.1, EDO.7 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Y.335, B:G.275, B:R.313, B:Y.335 Water bridges: A:G.275, A:Y.335

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 10 residues within 4Å: Chain A: I.267, Y.271, G.272, G.273, W.274, G.275, A.276, H.277 Chain B: A.276, H.277 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.270, A:T.270, A:Y.271, A:G.273, A:G.275, B:H.277 EDO.3: 8 residues within 4Å: Chain A: M.138, F.139, T.270, H.277, G.278, F.282, A.295, F.380 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.139, A:G.278 Water bridges: A:L.137, A:G.279 EDO.4: 2 residues within 4Å: Chain A: Q.187, R.199 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.187, A:Q.187 EDO.5: 5 residues within 4Å: Chain A: E.326, H.350, F.353, D.354, L.355 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.350, A:H.350, A:L.355 EDO.6: 3 residues within 4Å: Chain A: D.144, T.146, K.307 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.144 EDO.7: 8 residues within 4Å: Chain A: G.273, W.274, G.275, R.313 Chain B: F.139, A.276, L.315 Ligands: PEG.8 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.275, A:G.275, A:R.313 Water bridges: A:Y.335, A:Y.335, B:Q.317 EDO.9: 8 residues within 4Å: Chain B: L.137, M.138, F.139, T.270, H.277, G.278, F.282, A.295 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.137, B:F.139, B:G.278, B:G.279 EDO.10: 4 residues within 4Å: Chain B: T.146, E.148, I.155, K.159 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.148, B:K.159 Water bridges: B:E.147

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Panmanee, J. et al., Structural basis of the dominant inheritance of hypermethioninemia associated with the Arg264His mutation in the MAT1A gene. Acta Crystallogr D Struct Biol (2020)

Release Date

2020-06-17

Peptides

S-adenosylmethionine synthase isoform type-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

S-adenosylmethionine synthase isoform type-1

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