SMTL ID : 5a1g.1

The structure of Human MAT2A in complex with S-adenosylethionine and PPNP.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

homo-tetramer

Ligands

8 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.1: 7 residues within 4Å: Chain A: F.20, G.273, W.274, G.275, R.313, Y.335 Chain D: F.333 8 PLIP interactions: 1 interactions with chain D, 7 interactions with chain A Hydrophobic interactions: D:F.333, A:F.20, A:Y.335 Hydrogen bonds: A:G.275, A:R.313, A:R.313, A:Y.335, A:Y.335 MPD.2: 5 residues within 4Å: Chain A: H.158, K.159, A.162, Y.377, R.382 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.377 MPD.9: 7 residues within 4Å: Chain B: F.20, G.273, W.274, G.275, R.313, Y.335 Chain C: F.333 7 PLIP interactions: 1 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: C:F.333, B:F.20, B:Y.335 Hydrogen bonds: B:G.275, B:R.313, B:R.313, B:Y.335 MPD.10: 5 residues within 4Å: Chain B: H.158, K.159, A.162, Y.377, R.382 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.377 MPD.17: 7 residues within 4Å: Chain B: F.333 Chain C: F.20, G.273, W.274, G.275, R.313, Y.335 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:F.20, C:Y.335, B:F.333 Hydrogen bonds: C:G.275, C:R.313, C:R.313, C:Y.335 MPD.18: 5 residues within 4Å: Chain C: H.158, K.159, A.162, Y.377, R.382 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.377 MPD.25: 7 residues within 4Å: Chain A: F.333 Chain D: F.20, G.273, W.274, G.275, R.313, Y.335 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:F.20, D:Y.335, A:F.333 Hydrogen bonds: D:G.275, D:R.313, D:R.313, D:Y.335, D:Y.335 MPD.26: 5 residues within 4Å: Chain D: H.158, K.159, A.162, Y.377, R.382 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:Y.377

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

PPK.3: 16 residues within 4Å: Chain A: H.29, D.31, K.181, D.258, R.264, K.265 Chain D: D.134, G.279, G.280, A.281, K.285, D.291 Ligands: S7M.5, K.6, MG.7, MG.8 15 PLIP interactions: 7 interactions with chain D, 8 interactions with chain A Hydrogen bonds: D:A.281, D:K.285, D:K.285, A:D.258, A:R.264, A:R.264, A:K.265 Water bridges: D:D.134, D:D.134, D:D.134, D:D.291, A:K.181 Salt bridges: A:H.29, A:K.181, A:K.265 PPK.11: 16 residues within 4Å: Chain B: H.29, D.31, K.181, D.258, R.264, K.265 Chain C: D.134, G.279, G.280, A.281, K.285, D.291 Ligands: S7M.13, K.14, MG.15, MG.16 11 PLIP interactions: 8 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:D.258, B:R.264, B:R.264, B:K.265, C:A.281, C:K.285, C:K.285 Water bridges: B:K.181 Salt bridges: B:H.29, B:K.181, B:K.265 PPK.19: 16 residues within 4Å: Chain B: D.134, G.279, G.280, A.281, K.285, D.291 Chain C: H.29, D.31, K.181, D.258, R.264, K.265 Ligands: S7M.21, K.22, MG.23, MG.24 11 PLIP interactions: 8 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:D.258, C:R.264, C:R.264, C:K.265, B:A.281, B:K.285, B:K.285 Water bridges: C:K.181 Salt bridges: C:H.29, C:K.181, C:K.265 PPK.27: 16 residues within 4Å: Chain A: D.134, G.279, G.280, A.281, K.285, D.291 Chain D: H.29, D.31, K.181, D.258, R.264, K.265 Ligands: S7M.29, K.30, MG.31, MG.32 18 PLIP interactions: 7 interactions with chain A, 11 interactions with chain D Hydrogen bonds: A:A.281, A:K.285, A:K.285, D:D.258, D:R.264, D:R.264, D:R.264, D:K.265 Water bridges: A:D.134, A:D.134, A:D.134, A:D.291, D:D.31, D:D.31, D:K.181 Salt bridges: D:H.29, D:K.181, D:K.265

4 x IMD: IMIDAZOLE(Non-covalent)

IMD.4: 4 residues within 4Å: Chain A: F.18, Q.190 Chain D: F.333, E.342 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.193 IMD.12: 4 residues within 4Å: Chain B: F.18, Q.190 Chain C: F.333, E.342 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Water bridges: B:G.193, C:E.342 IMD.20: 4 residues within 4Å: Chain B: F.333, E.342 Chain C: F.18, Q.190 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Water bridges: C:G.193, B:E.342 IMD.28: 4 residues within 4Å: Chain A: F.333, E.342 Chain D: F.18, Q.190 1 PLIP interactions: 1 interactions with chain D Water bridges: D:G.193

4 x S7M: [(3S)-3-amino-3-carboxypropyl]{[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}ethyls ulfonium(Non-covalent)

S7M.5: 20 residues within 4Å: Chain A: H.29, P.30, D.179, K.181, S.206, S.247, R.249, F.250, I.252, D.258 Chain D: A.55, E.70, Q.113, D.116, I.117, G.133, D.134, K.289, I.322 Ligands: PPK.3 17 PLIP interactions: 10 interactions with chain A, 7 interactions with chain D Hydrogen bonds: A:D.179, A:S.247, A:R.249, A:D.258, D:E.70 Water bridges: A:S.206, A:S.247, A:A.259, D:K.289, D:K.289 Salt bridges: A:D.258, D:D.134, D:K.289 pi-Stacking: A:F.250, A:F.250 Hydrophobic interactions: D:D.134, D:I.322 S7M.13: 20 residues within 4Å: Chain B: H.29, P.30, D.179, K.181, S.206, S.247, R.249, F.250, I.252, D.258 Chain C: A.55, E.70, Q.113, D.116, I.117, G.133, D.134, K.289, I.322 Ligands: PPK.11 19 PLIP interactions: 10 interactions with chain B, 9 interactions with chain C Hydrogen bonds: B:D.179, B:S.247, B:R.249, B:D.258, C:E.70, C:E.70 Water bridges: B:S.206, B:S.247, B:A.259, C:D.134, C:K.289, C:K.289 Salt bridges: B:D.258, C:D.134, C:K.289 pi-Stacking: B:F.250, B:F.250 Hydrophobic interactions: C:D.134, C:I.322 S7M.21: 20 residues within 4Å: Chain B: A.55, E.70, Q.113, D.116, I.117, G.133, D.134, K.289, I.322 Chain C: H.29, P.30, D.179, K.181, S.206, S.247, R.249, F.250, I.252, D.258 Ligands: PPK.19 19 PLIP interactions: 10 interactions with chain C, 9 interactions with chain B Hydrogen bonds: C:D.179, C:S.247, C:R.249, C:D.258, B:E.70, B:E.70 Water bridges: C:S.206, C:S.247, C:A.259, B:D.134, B:K.289, B:K.289 Salt bridges: C:D.258, B:D.134, B:K.289 pi-Stacking: C:F.250, C:F.250 Hydrophobic interactions: B:D.134, B:I.322 S7M.29: 20 residues within 4Å: Chain A: A.55, E.70, Q.113, D.116, I.117, G.133, D.134, K.289, I.322 Chain D: H.29, P.30, D.179, K.181, S.206, S.247, R.249, F.250, I.252, D.258 Ligands: PPK.27 19 PLIP interactions: 12 interactions with chain D, 7 interactions with chain A Hydrogen bonds: D:D.179, D:S.247, D:R.249, D:D.258, D:D.258, D:D.258, A:E.70 Water bridges: D:S.206, D:S.247, D:A.259, A:K.289, A:K.289 Salt bridges: D:D.258, A:D.134, A:K.289 pi-Stacking: D:F.250, D:F.250 Hydrophobic interactions: A:D.134, A:I.322

4 x K: POTASSIUM ION(Non-covalent)

K.6: 5 residues within 4Å: Chain A: D.258, A.259 Chain D: E.57 Ligands: PPK.3, MG.7 4 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: D:E.57, A:D.258, A:A.259, H2O.34 K.14: 5 residues within 4Å: Chain B: D.258, A.259 Chain C: E.57 Ligands: PPK.11, MG.15 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:D.258, B:A.259, C:E.57, H2O.23 K.22: 5 residues within 4Å: Chain B: E.57 Chain C: D.258, A.259 Ligands: PPK.19, MG.23 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: C:D.258, C:A.259, B:E.57, H2O.13 K.30: 5 residues within 4Å: Chain A: E.57 Chain D: D.258, A.259 Ligands: PPK.27, MG.31 4 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: D:D.258, D:A.259, A:E.57, H2O.2

8 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 4 residues within 4Å: Chain A: D.31, K.265 Ligands: PPK.3, K.6 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.31, H2O.1, H2O.1 MG.8: 3 residues within 4Å: Chain A: K.265 Chain D: D.291 Ligands: PPK.3 No protein-ligand interaction detected (PLIP) MG.15: 4 residues within 4Å: Chain B: D.31, K.265 Ligands: PPK.11, K.14 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.31, H2O.12, H2O.12 MG.16: 3 residues within 4Å: Chain B: K.265 Chain C: D.291 Ligands: PPK.11 No protein-ligand interaction detected (PLIP) MG.23: 4 residues within 4Å: Chain C: D.31, K.265 Ligands: PPK.19, K.22 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.31, H2O.22, H2O.22 MG.24: 3 residues within 4Å: Chain B: D.291 Chain C: K.265 Ligands: PPK.19 No protein-ligand interaction detected (PLIP) MG.31: 4 residues within 4Å: Chain D: D.31, K.265 Ligands: PPK.27, K.30 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.31, H2O.33, H2O.33 MG.32: 3 residues within 4Å: Chain A: D.291 Chain D: K.265 Ligands: PPK.27 No protein-ligand interaction detected (PLIP)

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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

S-ADENOSYLMETHIONINE SYNTHASE ISOFORM TYPE-2

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