SMTL ID : 5a19.1

The structure of MAT2A in complex with PPNP.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.34 Å

Oligo State

homo-dimer

Ligands

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

PEG.1: 2 residues within 4Å: Chain A: V.77, D.78 No protein-ligand interaction detected (PLIP) PEG.2: 4 residues within 4Å: Chain A: H.326, P.327, L.328, I.330 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.328 Water bridges: A:I.330 PEG.3: 4 residues within 4Å: Chain A: H.158, K.159, A.162, R.382 No protein-ligand interaction detected (PLIP) PEG.7: 5 residues within 4Å: Chain A: F.18, Q.190, V.195, R.313 Chain B: F.333 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.313, A:R.313 PEG.10: 2 residues within 4Å: Chain B: V.77, D.78 No protein-ligand interaction detected (PLIP) PEG.11: 4 residues within 4Å: Chain B: H.326, P.327, L.328, I.330 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.328 Water bridges: B:I.330 PEG.12: 4 residues within 4Å: Chain B: H.158, K.159, A.162, R.382 No protein-ligand interaction detected (PLIP) PEG.16: 5 residues within 4Å: Chain A: F.333 Chain B: F.18, Q.190, V.195, R.313 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.313, B:R.313

2 x PPK: (DIPHOSPHONO)AMINOPHOSPHONIC ACID(Non-covalent)

PPK.4: 13 residues within 4Å: Chain A: E.23, H.29, D.31, K.181, D.258, R.264, K.265 Chain B: D.134, G.280, A.281, K.285, D.291 Ligands: MG.8 15 PLIP interactions: 9 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:K.181, A:D.258, A:R.264, A:K.265, A:K.265, B:D.134, B:A.281 Water bridges: A:R.264, A:R.264, B:K.285, B:D.291, B:D.291 Salt bridges: A:R.264, A:K.265, B:K.285 PPK.13: 13 residues within 4Å: Chain A: D.134, G.280, A.281, K.285, D.291 Chain B: E.23, H.29, D.31, K.181, D.258, R.264, K.265 Ligands: MG.17 16 PLIP interactions: 10 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:K.181, B:D.258, B:D.258, B:R.264, B:K.265, B:K.265, A:D.134, A:A.281 Water bridges: B:R.264, B:R.264, A:K.285, A:D.291, A:D.291 Salt bridges: B:R.264, B:K.265, A:K.285

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

EDO.5: 2 residues within 4Å: Chain A: K.350, K.351 No protein-ligand interaction detected (PLIP) EDO.14: 2 residues within 4Å: Chain B: K.350, K.351 No protein-ligand interaction detected (PLIP)

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

PG4.6: 5 residues within 4Å: Chain A: Q.36, H.89, Q.372, R.373, Y.377 No protein-ligand interaction detected (PLIP) PG4.15: 5 residues within 4Å: Chain B: Q.36, H.89, Q.372, R.373, Y.377 No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 5 residues within 4Å: Chain A: D.31, R.264, K.265 Ligands: PPK.4, K.9 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.31, H2O.1, H2O.1, H2O.6 MG.17: 5 residues within 4Å: Chain B: D.31, R.264, K.265 Ligands: PPK.13, K.18 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.31, H2O.7, H2O.7, H2O.12

2 x K: POTASSIUM ION(Non-covalent)

K.9: 4 residues within 4Å: Chain A: D.258, A.259 Chain B: E.57 Ligands: MG.8 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:D.258, B:E.57, H2O.4, H2O.6 K.18: 4 residues within 4Å: Chain A: E.57 Chain B: D.258, A.259 Ligands: MG.17 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:E.57, B:D.258, H2O.10, H2O.12

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Murray, B. et al., Crystallography Captures Catalytic Steps in Human Methionine Adenosyltransferase Enzymes. Proc.Natl.Acad.Sci.USA (2016)

Release Date

2016-02-17

Peptides

S-ADENOSYLMETHIONINE SYNTHASE ISOFORM TYPE-2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

S-ADENOSYLMETHIONINE SYNTHASE ISOFORM TYPE-2

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