SMTL ID : 4ktv.1

Structural insights of MAT enzymes: MATa2b complexed with adenosine and pyrophosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

hetero-4-2-mer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: F.334, H.335, Y.336 Chain B: Q.191 Chain F: T.324, V.325 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 interactions with chain F Hydrogen bonds: A:H.335, A:Y.336, B:Q.191, F:V.325 EDO.2: 3 residues within 4Å: Chain A: Q.81, K.82, R.85 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.82 EDO.5: 8 residues within 4Å: Chain A: T.18, F.19, L.20 Chain B: I.331, S.332, I.333, E.343, L.347 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:L.20, B:S.332, B:I.333 EDO.6: 6 residues within 4Å: Chain B: V.78, D.79, Y.80, V.109 Chain D: V.109, L.111 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.79, B:D.79, B:Y.80 EDO.7: 8 residues within 4Å: Chain B: Q.81, R.85, N.106, V.107 Chain C: K.62, T.63 Chain D: A.110, E.112 7 PLIP interactions: 2 interactions with chain C, 5 interactions with chain B Hydrogen bonds: C:T.63, C:T.63, B:Q.81, B:Q.81, B:R.85, B:N.106, B:V.107 EDO.8: 8 residues within 4Å: Chain A: G.258, D.259 Chain B: A.56, E.71, Q.114, I.118, K.290 Ligands: ADN.3 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.71, B:K.290 EDO.9: 5 residues within 4Å: Chain C: M.139, F.140, Y.272, A.277, H.278 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:F.140, C:A.277, C:G.279 EDO.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.13: 4 residues within 4Å: Chain A: K.103 Chain D: S.96, S.97, Q.257 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.96 EDO.14: 7 residues within 4Å: Chain C: G.258, D.259 Chain D: E.71, Q.114, I.118, K.290 Ligands: ADN.11 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.114 EDO.15: 7 residues within 4Å: Chain C: T.18, F.19, L.20 Chain D: S.332, I.333, E.343, L.347 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:I.331, D:I.333, D:E.343, D:E.343, C:L.20 EDO.17: 5 residues within 4Å: Chain E: P.92, A.189, R.212, K.251, R.282 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:R.212, E:R.282, E:R.282

2 x ADN: ADENOSINE(Non-covalent)

ADN.3: 15 residues within 4Å: Chain A: H.30, P.31, D.180, K.182, S.207, S.248, R.250, F.251, I.253, D.259 Chain B: D.117, I.118, D.135, I.323 Ligands: EDO.8 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.180, A:S.248, A:R.250, A:D.259, A:D.259 pi-Stacking: A:F.251, A:F.251 ADN.11: 15 residues within 4Å: Chain C: H.30, P.31, D.180, K.182, S.248, R.250, F.251, I.253, D.259 Chain D: D.117, I.118, D.135, I.323 Ligands: POP.12, EDO.14 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:D.180, C:S.248, C:R.250, C:D.259, D:G.134 pi-Stacking: C:F.251, C:F.251

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

PO4.4: 7 residues within 4Å: Chain A: H.30, D.32, D.259, R.265, K.266 Chain B: K.286, D.292 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Salt bridges: B:K.286, A:R.265, A:K.266 Hydrogen bonds: A:D.32, A:D.32, A:D.32

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

POP.12: 12 residues within 4Å: Chain C: E.24, H.30, D.32, K.182, D.259, K.266 Chain D: D.135, Q.136, G.280, D.292 Ligands: ADN.11, MG.16 10 PLIP interactions: 6 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:E.24, D:D.135, D:G.280 Salt bridges: C:H.30, C:K.182, C:K.182, C:K.266, C:K.266, D:K.286, D:K.286

1 x MG: MAGNESIUM ION(Non-covalent)

MG.16: 6 residues within 4Å: Chain C: R.265 Chain D: G.280, A.282, K.286, D.292 Ligands: POP.12 No protein-ligand interaction detected (PLIP)

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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