SMTL ID : 6rkc.1 (1 other biounit)

Inter-dimeric interface controls function and stability of S-methionine adenosyltransferase from U. urealiticum

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.56 Å

Oligo State

homo-tetramer

Ligands

3 x K: POTASSIUM ION(Non-covalent)

K.1: 5 residues within 4Å: Chain A: D.231, T.232 Chain B: E.44 Ligands: MG.2, PPK.5 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Metal complexes: B:E.44, A:D.231 K.8: 5 residues within 4Å: Chain A: E.44 Chain B: D.231, T.232 Ligands: PPK.9, MG.10 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Metal complexes: A:E.44, B:D.231 K.13: 5 residues within 4Å: Chain C: D.231, T.232 Chain D: E.44 Ligands: MG.14, PPK.17 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Metal complexes: D:E.44, C:D.231

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.18, D.231, T.232 Ligands: K.1, PPK.5 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.18 MG.3: 5 residues within 4Å: Chain A: D.113, D.264 Chain B: E.10, K.160 Ligands: PPK.9 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain B: D.113, D.264 Ligands: PPK.5 No protein-ligand interaction detected (PLIP) MG.10: 6 residues within 4Å: Chain B: D.18, D.231, T.232, K.238 Ligands: K.8, PPK.9 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.18, B:D.18 MG.14: 5 residues within 4Å: Chain C: D.18, T.232, R.237 Ligands: K.13, PPK.17 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.18, C:D.18 MG.15: 5 residues within 4Å: Chain C: D.113, Q.114, D.264 Chain D: K.160 Ligands: PPK.20 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.113, C:D.264 MG.19: 3 residues within 4Å: Chain D: G.253, D.264 Ligands: PPK.17 No protein-ligand interaction detected (PLIP) MG.21: 4 residues within 4Å: Chain D: D.18, R.237, K.238 Ligands: PPK.20 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.18, D:D.18

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

SAM.4: 19 residues within 4Å: Chain A: H.16, P.17, D.158, K.160, S.180, S.220, R.222, F.223, D.231 Chain B: A.42, E.57, Q.93, D.96, I.97, G.112, D.113, K.262, I.295 Ligands: PPK.5 13 PLIP interactions: 7 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:D.158, A:S.220, A:R.222, A:D.231, B:E.57, B:E.57 Salt bridges: A:D.231, B:D.113, B:K.262 pi-Stacking: A:F.223, A:F.223 Water bridges: B:E.44, B:K.262 SAM.6: 13 residues within 4Å: Chain A: I.58, T.59, T.60, H.61, A.62, Y.63, V.64, V.66, V.90, K.92 Chain D: W.71, E.81, N.82 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:Y.63 Hydrogen bonds: A:I.58, A:T.60, A:T.60, A:V.64, A:V.64, D:E.81, D:N.82 Water bridges: A:V.90 Salt bridges: D:E.81 pi-Stacking: D:W.71 SAM.11: 19 residues within 4Å: Chain A: A.42, E.57, Q.93, D.96, I.97, G.112, D.113, K.262, I.295 Chain B: H.16, P.17, D.158, K.160, S.220, R.222, F.223, I.225, D.231 Ligands: PPK.9 15 PLIP interactions: 8 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:E.57, A:E.57, B:D.158, B:S.220, B:R.222, B:D.231 Water bridges: A:S.94, A:I.97, A:K.262, A:K.262 Salt bridges: A:D.113, A:K.262, B:D.231 pi-Stacking: B:F.223, B:F.223 SAM.12: 13 residues within 4Å: Chain B: I.58, T.59, T.60, H.61, A.62, Y.63, V.64, V.66, V.90, K.92 Chain C: W.71, E.81, N.82 10 PLIP interactions: 3 interactions with chain C, 7 interactions with chain B Hydrogen bonds: C:N.82, B:I.58, B:T.60, B:T.60, B:V.64, B:V.64, B:K.92 Salt bridges: C:E.81, B:H.61 pi-Stacking: C:W.71 SAM.16: 20 residues within 4Å: Chain C: H.16, P.17, D.158, K.160, S.180, S.220, R.222, F.223, I.225, D.231 Chain D: A.42, E.57, Q.93, D.96, I.97, G.112, D.113, K.262, I.295 Ligands: PPK.17 16 PLIP interactions: 9 interactions with chain C, 7 interactions with chain D Hydrogen bonds: C:D.158, C:S.220, C:R.222, C:D.231, C:D.231, D:E.57, D:Q.93 Water bridges: C:S.180, D:I.97, D:I.97, D:Q.114 Salt bridges: C:D.231, D:D.113, D:K.262 pi-Stacking: C:F.223, C:F.223 SAM.18: 14 residues within 4Å: Chain B: W.71, E.81, N.82 Chain C: I.58, T.59, T.60, H.61, A.62, Y.63, V.64, V.66, V.90, N.91, K.92 10 PLIP interactions: 7 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:I.58, C:T.60, C:T.60, C:V.64, C:V.64, B:N.82 Water bridges: C:V.90 Salt bridges: C:H.61, B:E.81 pi-Stacking: B:W.71 SAM.22: 19 residues within 4Å: Chain C: A.42, E.57, Q.93, D.96, I.97, G.112, D.113, K.262, I.295 Chain D: H.16, P.17, D.158, K.160, S.220, R.222, F.223, I.225, D.231 Ligands: PPK.20 15 PLIP interactions: 5 interactions with chain C, 10 interactions with chain D Hydrogen bonds: C:Q.93, D:D.158, D:S.220, D:R.222, D:D.231, D:D.231, D:D.231 Water bridges: C:K.262, C:K.262, D:S.180 Salt bridges: C:D.113, C:K.262, D:D.231 pi-Stacking: D:F.223, D:F.223 SAM.23: 13 residues within 4Å: Chain A: W.71, E.81, N.82 Chain D: I.58, T.59, T.60, H.61, A.62, Y.63, V.64, V.66, V.90, K.92 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain D Hydrogen bonds: A:N.82, D:I.58, D:T.60, D:T.60, D:H.61, D:V.64, D:V.64 Salt bridges: A:E.81 pi-Stacking: A:W.71

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

PPK.5: 16 residues within 4Å: Chain A: H.16, D.18, K.160, D.231, R.237, K.238 Chain B: D.113, G.252, G.253, A.254, K.258, D.264 Ligands: K.1, MG.2, SAM.4, MG.7 13 PLIP interactions: 5 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:R.237, A:K.238, B:D.113, B:D.113, B:G.252, B:A.254, B:K.258, B:K.258, B:K.258 Salt bridges: A:H.16, A:K.160, A:K.238 Water bridges: B:E.44 PPK.9: 15 residues within 4Å: Chain A: D.113, G.253, A.254, K.258, D.264 Chain B: H.16, D.18, K.160, D.231, R.237, K.238 Ligands: MG.3, K.8, MG.10, SAM.11 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:G.252, A:A.254, A:K.258, A:K.258, B:R.237, B:K.238 Salt bridges: B:H.16, B:K.160, B:K.238 PPK.17: 15 residues within 4Å: Chain C: H.16, D.18, K.160, D.231, R.237, K.238 Chain D: D.113, G.253, A.254, K.258, D.264 Ligands: K.13, MG.14, SAM.16, MG.19 14 PLIP interactions: 5 interactions with chain D, 9 interactions with chain C Hydrogen bonds: D:A.254, D:K.258, D:K.258, D:K.258, D:D.264, C:D.231, C:D.231, C:R.237, C:R.237, C:K.238 Water bridges: C:K.160 Salt bridges: C:H.16, C:K.160, C:K.238 PPK.20: 14 residues within 4Å: Chain C: D.113, G.253, A.254, K.258, D.264 Chain D: H.16, D.18, K.160, D.231, R.237, K.238 Ligands: MG.15, MG.21, SAM.22 11 PLIP interactions: 5 interactions with chain D, 6 interactions with chain C Hydrogen bonds: D:D.231, D:R.237, C:G.252, C:A.254, C:K.258, C:K.258, C:K.258, C:D.264 Salt bridges: D:H.16, D:K.160, D:K.238

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kleiner, D. et al., The interdimeric interface controls function and stability of Ureaplasma urealiticum methionine S-adenosyltransferase. J.Mol.Biol. (2019)

Release Date

2019-09-25

Peptides

Methionine adenosyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Methionine adenosyltransferase

Related Entries With Identical Sequence