SMTL ID : 2obv.2 (1 other biounit)

Crystal structure of the human S-adenosylmethionine synthetase 1 in complex with the product

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-tetramer

Ligands

8 x NA: SODIUM ION(Non-functional Binders)

NA.1: 2 residues within 4Å: Chain A: A.151, D.155 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.155 Water bridges: A:R.158 NA.2: 1 residues within 4Å: Chain A: E.205 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.205 NA.7: 2 residues within 4Å: Chain B: A.151, D.155 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.151 Water bridges: B:R.158 NA.8: 1 residues within 4Å: Chain B: E.205 No protein-ligand interaction detected (PLIP) NA.13: 2 residues within 4Å: Chain C: A.151, D.155 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.151 Water bridges: C:R.158 NA.14: 1 residues within 4Å: Chain C: E.205 No protein-ligand interaction detected (PLIP) NA.19: 2 residues within 4Å: Chain D: A.151, D.155 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:A.151 Water bridges: D:R.158 NA.20: 1 residues within 4Å: Chain D: E.205 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.205

4 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.3: 19 residues within 4Å: Chain A: H.18, P.19, D.168, K.170, S.195, S.236, R.238, F.239, I.241, D.247 Chain B: A.44, E.59, Q.102, D.105, I.106, G.122, D.123, K.278, I.311 20 PLIP interactions: 11 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:D.168, A:S.236, A:R.238, A:D.247, A:D.247, B:E.59, B:E.59, B:Q.102 Water bridges: A:S.195, A:S.236, A:A.248, B:I.106, B:I.106, B:K.278, B:K.278 Salt bridges: A:D.247, B:D.123, B:K.278 pi-Stacking: A:F.239, A:F.239 SAM.9: 19 residues within 4Å: Chain A: A.44, E.59, Q.102, D.105, I.106, G.122, D.123, K.278, I.311 Chain B: H.18, P.19, D.168, K.170, S.195, S.236, R.238, F.239, I.241, D.247 20 PLIP interactions: 9 interactions with chain A, 11 interactions with chain B Hydrogen bonds: A:E.59, A:E.59, A:Q.102, B:D.168, B:S.236, B:R.238, B:D.247, B:D.247 Water bridges: A:I.106, A:I.106, A:K.278, A:K.278, B:S.195, B:S.236, B:A.248 Salt bridges: A:D.123, A:K.278, B:D.247 pi-Stacking: B:F.239, B:F.239 SAM.15: 19 residues within 4Å: Chain C: H.18, P.19, D.168, K.170, S.195, S.236, R.238, F.239, I.241, D.247 Chain D: A.44, E.59, Q.102, D.105, I.106, G.122, D.123, K.278, I.311 22 PLIP interactions: 11 interactions with chain C, 11 interactions with chain D Hydrogen bonds: C:D.168, C:S.236, C:R.238, C:D.247, C:D.247, D:E.59, D:E.59, D:E.59, D:Q.102 Water bridges: C:S.195, C:S.236, C:A.248, D:I.106, D:I.106, D:D.123, D:K.278, D:K.278 Salt bridges: C:D.247, D:D.123, D:K.278 pi-Stacking: C:F.239, C:F.239 SAM.21: 19 residues within 4Å: Chain C: A.44, E.59, Q.102, D.105, I.106, G.122, D.123, K.278, I.311 Chain D: H.18, P.19, D.168, K.170, S.195, S.236, R.238, F.239, I.241, D.247 22 PLIP interactions: 11 interactions with chain C, 11 interactions with chain D Hydrogen bonds: C:E.59, C:E.59, C:E.59, C:Q.102, D:D.168, D:S.236, D:R.238, D:D.247, D:D.247 Water bridges: C:I.106, C:I.106, C:D.123, C:K.278, C:K.278, D:S.195, D:S.236, D:A.248 Salt bridges: C:D.123, C:K.278, D:D.247 pi-Stacking: D:F.239, D:F.239

12 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.4: 10 residues within 4Å: Chain A: F.7, Q.179, G.182, V.184, W.263, R.302 Chain B: L.304, F.322, Y.324 Ligands: PG4.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.302 Water bridges: A:G.264, A:Y.324 PG4.5: 8 residues within 4Å: Chain A: E.137, I.144, H.147, K.148, A.151, Y.366, G.370, R.371 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.137, A:K.148 PG4.6: 6 residues within 4Å: Chain A: D.133, T.135, E.136, C.138, V.295, K.296 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.136, A:K.296 Water bridges: A:E.136 PG4.10: 10 residues within 4Å: Chain A: L.304, F.322, Y.324 Chain B: F.7, Q.179, G.182, V.184, W.263, R.302 Ligands: PG4.4 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.302 Water bridges: B:G.264, B:Y.324 PG4.11: 8 residues within 4Å: Chain B: E.137, I.144, H.147, K.148, A.151, Y.366, G.370, R.371 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.137, B:K.148 PG4.12: 6 residues within 4Å: Chain B: D.133, T.135, E.136, C.138, V.295, K.296 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.136, B:K.296 Water bridges: B:E.136 PG4.16: 10 residues within 4Å: Chain C: F.7, Q.179, G.182, V.184, W.263, R.302 Chain D: L.304, F.322, Y.324 Ligands: PG4.22 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.302 Water bridges: C:G.264, C:R.302 PG4.17: 8 residues within 4Å: Chain C: E.137, I.144, H.147, K.148, A.151, Y.366, G.370, R.371 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.148 PG4.18: 6 residues within 4Å: Chain C: D.133, T.135, E.136, C.138, V.295, K.296 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.136, C:K.296 Water bridges: C:E.136 PG4.22: 10 residues within 4Å: Chain C: L.304, F.322, Y.324 Chain D: F.7, Q.179, G.182, V.184, W.263, R.302 Ligands: PG4.16 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.302 Water bridges: D:G.264, D:R.302 PG4.23: 8 residues within 4Å: Chain D: E.137, I.144, H.147, K.148, A.151, Y.366, G.370, R.371 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.148 PG4.24: 6 residues within 4Å: Chain D: D.133, T.135, E.136, C.138, V.295, K.296 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.136, D:K.296 Water bridges: D:E.136

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pilka, E.S. et al., Crystal structure of the human S-adenosylmethionine synthetase 1 in complex with the product. To be Published

Release Date

2007-01-02

Peptides

S-adenosylmethionine synthetase isoform type-1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

S-adenosylmethionine synthetase isoform type-1

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