SMTL ID : 4ndn.1

Structural insights of MAT enzymes: MATa2b complexed with SAM and PPNP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.34 Å

Oligo State

hetero-4-2-mer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.31, R.264, K.265 Ligands: MG.2, PPK.6 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.31, H2O.2, H2O.4 MG.2: 3 residues within 4Å: Chain B: K.285 Ligands: MG.1, PPK.6 No protein-ligand interaction detected (PLIP) MG.13: 5 residues within 4Å: Chain C: D.31, R.264, K.265 Ligands: PPK.16, MG.18 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.31, H2O.9, H2O.10 MG.18: 3 residues within 4Å: Chain D: K.285 Ligands: MG.13, PPK.16 No protein-ligand interaction detected (PLIP)

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

EDO.3: 4 residues within 4Å: Chain A: A.162, A.165, E.166, R.169 Ligand excluded by PLIP EDO.4: 8 residues within 4Å: Chain A: E.27, Q.36, H.89, Q.372, R.373, A.376, Y.377, R.382 Ligand excluded by PLIP EDO.5: 9 residues within 4Å: Chain A: G.69, E.70, A.109, E.111 Chain B: K.61, T.62, G.257, D.258, A.259 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: K.61, Q.256 Chain B: E.111, Q.112, S.114, P.115 Ligand excluded by PLIP EDO.9: 3 residues within 4Å: Chain B: V.108 Chain D: Y.79, V.108 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain B: D.191, R.192, A.194, R.312, T.337 Chain F: P.310 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain B: H.326, D.354, R.356 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain A: T.17, F.18 Chain B: S.331, I.332, E.342, R.343, L.346 Ligand excluded by PLIP EDO.14: 7 residues within 4Å: Chain C: M.138, F.139, T.270, H.277, G.278, F.282, F.380 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain C: L.328, S.329, I.330, L.346 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain D: R.219, Y.242, H.243, L.244 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain D: Q.36, H.89, Q.372, R.373, A.376, Y.377 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain B: D.78, Q.80 Chain D: I.71, Y.79, L.110, E.111 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain D: A.40, V.82, E.85, A.86, Q.372 Ligand excluded by PLIP EDO.23: 7 residues within 4Å: Chain D: R.192, R.312, G.336, T.337 Chain E: W.309, P.310, Q.319 Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain D: K.228, A.229, V.231, P.232 Ligand excluded by PLIP EDO.25: 7 residues within 4Å: Chain E: S.240, G.241, N.242, Q.283, L.284, C.286, R.297 Ligand excluded by PLIP

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

PPK.6: 16 residues within 4Å: Chain A: E.23, H.29, D.31, K.181, D.258, R.264, K.265 Chain B: D.134, G.279, G.280, A.281, K.285, D.291 Ligands: MG.1, MG.2, SAM.7 13 PLIP interactions: 6 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:R.264, A:R.264, A:K.265, B:G.279, B:A.281, B:K.285, B:D.291 Salt bridges: A:H.29, A:K.181, A:K.265 Water bridges: B:D.291, B:D.291, B:D.291 PPK.16: 16 residues within 4Å: Chain C: E.23, 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: MG.13, SAM.17, MG.18 14 PLIP interactions: 9 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:D.31, C:K.181, C:R.264, C:R.264, C:K.265, D:D.134, D:A.281, D:K.285, D:D.291 Water bridges: C:E.23, D:G.278 Salt bridges: C:H.29, C:K.181, C:K.265

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

SAM.7: 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 B: A.55, E.70, Q.113, D.116, I.117, G.133, D.134, K.289, I.322 Ligands: PPK.6 17 PLIP interactions: 11 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:D.179, A:S.247, A:R.249, A:D.258, A:D.258, B:E.70 Water bridges: A:S.206, A:S.247, A:D.258, B:D.134, B:K.289, B:K.289 Salt bridges: A:D.258, B:D.134, B:K.289 pi-Stacking: A:F.250, A:F.250 SAM.17: 19 residues within 4Å: Chain C: H.29, P.30, D.179, K.181, 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.16 21 PLIP interactions: 12 interactions with chain D, 9 interactions with chain C Hydrophobic interactions: D:I.117 Hydrogen bonds: D:E.70, D:Q.113, C:D.179, C:S.247, C:R.249, C:D.258, C:D.258 Water bridges: D:I.117, D:I.117, D:D.134, D:D.134, D:K.289, D:K.289, D:K.289, C:S.247 Salt bridges: D:D.134, D:K.289, C:D.258 pi-Stacking: C:F.250, C:F.250

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Murray, B. et al., Structure and function study of the complex that synthesizes S-adenosylmethionine. IUCrJ (2014)

Release Date

2014-07-16

Peptides

S-adenosylmethionine synthase isoform type-2: ABCD
Methionine adenosyltransferase 2 subunit beta: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

S-adenosylmethionine synthase isoform type-2

Methionine adenosyltransferase 2 subunit beta

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