SMTL ID : 5t8s.1

Crystal Structure of a S-adenosylmethionine Synthase from Neisseria gonorrhoeae with bound S-adenosylmethionine, AMP, Pyrophosphate, Phosphate, and Magnesium

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.284 Chain B: E.17, K.258 Ligands: 3PO.9 No protein-ligand interaction detected (PLIP) MG.3: 4 residues within 4Å: Chain A: D.25, K.258 Ligands: POP.4, PO4.5 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.25, H2O.1, H2O.6 MG.6: 3 residues within 4Å: Chain B: D.25, K.258 Ligands: 3PO.9 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.25, H2O.16, H2O.18 MG.8: 4 residues within 4Å: Chain B: K.278, D.284 Ligands: POP.4, PO4.5 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.284, H2O.10, H2O.19

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.2: 13 residues within 4Å: Chain A: H.23, P.24, D.174, K.176, S.199, T.240, R.242, F.243, D.251 Chain B: G.128, D.129, I.315 Ligands: POP.4 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:D.174, A:S.199, A:R.242, A:D.251 Water bridges: A:T.240, B:G.128, B:D.129, B:D.129 pi-Stacking: A:F.243, A:F.243

1 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.4: 11 residues within 4Å: Chain A: H.23, D.25, K.176, K.258 Chain B: D.129, K.278, D.284 Ligands: AMP.2, MG.3, PO4.5, MG.8 16 PLIP interactions: 7 interactions with chain A, 9 interactions with chain B Water bridges: A:K.176, A:K.176, A:K.176, B:D.129, B:D.129, B:D.129, B:D.129, B:K.278, B:K.278 Salt bridges: A:H.23, A:K.176, A:K.258, A:K.258, B:K.278 Hydrogen bonds: B:D.129, B:D.284

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 11 residues within 4Å: Chain A: D.25, R.257, K.258 Chain B: G.272, G.273, A.274, K.278, D.284 Ligands: MG.3, POP.4, MG.8 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Salt bridges: A:R.257, A:K.258, B:K.278 Hydrogen bonds: B:A.274, B:D.284, B:D.284

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

SAM.7: 19 residues within 4Å: Chain A: A.49, E.64, Q.107, D.110, I.111, G.128, D.129, K.282, I.315 Chain B: H.23, P.24, D.174, K.176, S.199, T.240, R.242, F.243, D.251 Ligands: 3PO.9 19 PLIP interactions: 10 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:D.174, B:S.199, B:T.240, B:D.251, B:D.251, B:D.251, A:E.64, A:Q.107 Water bridges: B:R.242, A:E.64, A:I.111, A:I.111, A:K.282, A:K.282 Salt bridges: B:D.251, A:D.129, A:K.282 pi-Stacking: B:F.243, B:F.243

1 x 3PO: TRIPHOSPHATE(Non-covalent)

3PO.9: 15 residues within 4Å: Chain A: D.129, G.272, G.273, A.274, K.278, D.284 Chain B: H.23, D.25, K.176, D.251, R.257, K.258 Ligands: MG.1, MG.6, SAM.7 17 PLIP interactions: 8 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:D.129, A:G.272, A:A.274, A:D.284, B:R.257, B:R.257 Water bridges: A:K.278, A:K.278, B:K.176 Salt bridges: A:K.278, A:K.278, B:H.23, B:K.176, B:R.257, B:K.258, B:K.258, B:K.258

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dranow, D.M. et al., Crystal Structure of a S-adenosylmethionine Synthase from Neisseria gonorrhoeae with bound S-adenosylmethionine, AMP, Pyrophosphate, Phosphate, and Magnesium. to be published

Release Date

2016-09-28

Peptides

S-adenosylmethionine synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

S-adenosylmethionine synthase

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