- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.40 Å
- Oligo State
- hetero-1-1-mer
- Ligands
- 8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 14 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
DMS.4: 3 residues within 4Å:- Chain A: F.82, F.114, R.117
1 PLIP interactions:1 interactions with chain A- Water bridges: A:N.109
DMS.5: 4 residues within 4Å:- Chain A: A.59, D.60, A.129, I.153
1 PLIP interactions:1 interactions with chain A- Salt bridges: A:D.60
DMS.6: 5 residues within 4Å:- Chain A: E.5, N.147, I.148, A.149, R.171
No protein-ligand interaction detected (PLIP)DMS.17: 5 residues within 4Å:- Chain B: Q.42, F.45, A.46, L.49, M.207
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:A.46
DMS.18: 2 residues within 4Å:- Chain B: R.363, E.364
No protein-ligand interaction detected (PLIP)DMS.19: 1 residues within 4Å:- Ligands: EDO.15
No protein-ligand interaction detected (PLIP)DMS.20: 6 residues within 4Å:- Chain B: Q.36, K.37, D.38, P.39, Q.42
- Ligands: EDO.11
No protein-ligand interaction detected (PLIP)DMS.21: 4 residues within 4Å:- Chain B: T.3, L.4, L.5, N.6
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:T.3
DMS.22: 5 residues within 4Å:- Chain B: P.56, E.211, A.214, Q.215
- Ligands: EDO.8
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:Q.215
DMS.23: 3 residues within 4Å:- Chain B: Y.8, G.10, E.11
3 PLIP interactions:3 interactions with chain B- Water bridges: B:Y.8
- Salt bridges: B:E.11
- pi-Cation interactions: B:Y.8
DMS.24: 3 residues within 4Å:- Chain B: I.262, H.267, H.273
No protein-ligand interaction detected (PLIP)DMS.25: 2 residues within 4Å:- Chain B: F.385, H.388
1 PLIP interactions:1 interactions with chain B- pi-Cation interactions: B:H.388
DMS.26: 8 residues within 4Å:- Chain B: P.270, L.271, K.272, H.273, G.274, R.275, V.276, P.285
1 PLIP interactions:1 interactions with chain B- Water bridges: B:V.276
DMS.27: 6 residues within 4Å:- Chain A: F.107, I.111, P.138, F.139
- Chain B: Y.16, K.283
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:K.283
- 2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
PEG.7: 3 residues within 4Å:- Chain B: G.10, E.11, F.12
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:E.11
- Water bridges: B:E.11
PEG.10: 6 residues within 4Å:- Chain B: L.59, T.60, K.61, Q.63, Y.74, K.219
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:L.59, B:K.61
- Water bridges: B:Y.74
- 2 x NA: SODIUM ION(Non-functional Binders)
- 1 x KOU: (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine(Non-covalent)
KOU.16: 23 residues within 4Å:- Chain B: A.85, H.86, K.87, T.110, G.111, A.112, G.113, Q.114, H.115, T.190, C.230, V.231, G.232, G.233, G.234, S.235, N.236, A.302, G.303, L.304, D.305, E.350, S.377
25 PLIP interactions:25 interactions with chain B- Hydrophobic interactions: B:A.85
- Hydrogen bonds: B:K.87, B:G.111, B:A.112, B:G.113, B:Q.114, B:H.115, B:T.190, B:G.232, B:G.233, B:G.234, B:S.235, B:N.236, B:N.236, B:D.305, B:S.377
- Water bridges: B:E.109, B:Q.114, B:G.234, B:A.237, B:E.350
- Salt bridges: B:H.86, B:K.87, B:K.87
- pi-Stacking: B:H.86
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Hilario, E. et al., The external aldimine form of the Salmonella thypi wild-type tryptophan synthase in open conformation showing multiple side chain conformations for the residue beta Q114 and sodium ion at the metal coordination site. One of the beta-Q114 rotamer conformations allows a hydrogen bond to form with the PLP oxygen at the position 3 in the ring. To be Published
- Release Date
- 2021-03-10
- Peptides
- Tryptophan synthase alpha chain: A
Tryptophan synthase beta chain: B - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B
SMTL ID : 6wdu.1
The external aldimine form of the Salmonella thypi wild-type tryptophan synthase in open conformation showing multiple side chain conformations for the residue beta Q114 and sodium ion at the metal coordination site. One of the beta-Q114 rotamer conformations allows a hydrogen bond to form with the PLP oxygen at the position 3 in the ring.
Tryptophan synthase alpha chain
Tryptophan synthase beta chain
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1a50.1 | 1a5s.1 | 1bks.1 | 1c29.1 | 1c8v.1 | 1c9d.1 | 1cw2.1 | 1cx9.1 | 1fuy.1 | 1k3u.1 | 1k7e.1 | 1k7f.1 | 1k7x.1 | 1k8x.1 | 1k8y.1 | 1k8z.1 | 1kfc.1 | 1kfj.1 | 1kfk.1 | 1qoq.1 | 1tjp.1 | 1ttp.1 | 1ttq.1 | 1ubs.1 | 2cle.1 | 2clf.1 | 2clh.1 | 2cli.1 | 2cll.1 | 2clm.1 more...less...2clo.1 | 2j9x.1 | 2j9y.1 | 2rh9.1 | 2rhg.1 | 2trs.1 | 2tsy.1 | 2tys.1 | 2wsy.1 | 4hn4.1 | 4hpj.1 | 4hpx.1 | 4hpx.2 | 4ht3.1 | 4kkx.1 | 4wx2.1 | 4xug.1 | 4y6g.1 | 4zqc.1 | 5bw6.1 | 5cgq.1 | 6c73.1 | 6d0v.1 | 6duc.1 | 6dz4.1 | 6dzo.1 | 6o1h.1 | 6oso.1 | 6ouy.1 | 6vfd.1 | 6vnt.1 | 6wx3.1 | 6x0c.1 | 6xe3.1 | 6xin.1 | 6xnc.1 | 6xoy.1 | 6xrh.1 | 6xsy.1 | 6xt0.1 | 7jhw.1 | 7jll.1 | 7jmq.1 | 7jmq.2 | 7jqw.1 | 7jtt.1 | 7k0b.1 | 7k5a.1 | 7ka1.1 | 7kbn.1 | 7kh6.1 | 7ki7.1 | 7kmc.1 | 7kq9.1 | 7kqf.1 | 7ku9.1 | 7kwv.1 | 7kxc.1 | 7kyt.1 | 7l03.1 | 7l1h.1 | 7l47.1 | 7l4d.1 | 7l5h.1 | 7lev.1 | 7lgx.1 | 7lkl.1 | 7lpf.1 | 7lt4.1 | 7ltp.1 | 7lut.1 | 7lv5.1 | 7lvx.1 | 7lx1.1 | 7ly8.1 | 7m2l.1 | 7m3s.1 | 7m3s.2 | 7me8.1 | 7mt4.1 | 7mt5.1 | 7mt6.1 | 8b03.1 | 8b05.1 | 8b06.1 | 8b08.1