SMTL ID : 3rv2.2 (1 other biounit)

Crystal structure of S-adenosylmethionine synthetase from Mycobacterium marinum

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

6 x CA: CALCIUM ION(Non-covalent)

CA.1: 1 residues within 4Å: Chain A: D.263 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.263, H2O.2, H2O.2, H2O.4, H2O.8 CA.2: 3 residues within 4Å: Chain A: D.398, D.401, D.402 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.401, A:D.401, A:D.402, H2O.2, H2O.2 CA.5: 1 residues within 4Å: Chain B: D.263 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.263, H2O.11, H2O.15, H2O.18, H2O.18 CA.10: 1 residues within 4Å: Chain C: D.263 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.263, H2O.22, H2O.22, H2O.24, H2O.27 CA.11: 3 residues within 4Å: Chain C: D.398, D.401, D.402 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.401, C:D.401, C:D.402, H2O.22, H2O.22 CA.14: 1 residues within 4Å: Chain D: D.263 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:D.263, H2O.31, H2O.35, H2O.37, H2O.37

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

EDO.3: 7 residues within 4Å: Chain A: H.162, R.163, R.166, G.386, R.387, T.388, D.389 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.386, A:T.388 Water bridges: A:R.163, A:R.167 EDO.6: 7 residues within 4Å: Chain B: H.162, R.163, R.166, G.386, R.387, T.388, D.389 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.386, B:T.388 Water bridges: B:R.163 EDO.7: 4 residues within 4Å: Chain B: W.305, D.368, D.398, K.399 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.368, B:D.398, B:K.399 EDO.8: 2 residues within 4Å: Chain B: R.367, D.368 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.367 EDO.12: 7 residues within 4Å: Chain C: H.162, R.163, R.166, G.386, R.387, T.388, D.389 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.386, C:T.388 Water bridges: C:R.163, C:R.167 EDO.15: 7 residues within 4Å: Chain D: H.162, R.163, R.166, G.386, R.387, T.388, D.389 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.386, D:T.388 Water bridges: D:R.163 EDO.16: 4 residues within 4Å: Chain D: W.305, D.368, D.398, K.399 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.368, D:D.398, D:K.399 EDO.17: 2 residues within 4Å: Chain D: R.367, D.368 1 PLIP interactions: 1 interactions with chain D Water bridges: D:R.367

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: R.45, V.46, A.47, E.62, V.63, T.64, K.294 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.47, A:T.64, A:K.294 Water bridges: A:Q.108 GOL.9: 7 residues within 4Å: Chain B: R.45, V.46, A.47, E.62, V.63, T.64, K.294 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.47, B:T.64, B:T.64, B:K.294, B:K.294 GOL.13: 7 residues within 4Å: Chain C: R.45, V.46, A.47, E.62, V.63, T.64, K.294 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:A.47, C:T.64, C:K.294 Water bridges: C:Q.108 GOL.18: 7 residues within 4Å: Chain D: R.45, V.46, A.47, E.62, V.63, T.64, K.294 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:A.47, D:T.64, D:T.64, D:K.294, D:K.294

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baugh, L. et al., Increasing the structural coverage of tuberculosis drug targets. Tuberculosis (Edinb) (2015)

Release Date

2011-05-18

Peptides

S-adenosylmethionine synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

S-adenosylmethionine synthase

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