SMTL ID : 7kq9.1

The aminoacrylate form of the beta-Q114A mutant Tryptophan Synthase at 1.50 Angstrom resolution with cesium ion at the metal coordination site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

hetero-1-1-mer

Ligands

5 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 4 residues within 4Å: Chain A: H.92, P.93, T.94, I.95 Ligand excluded by PLIP CL.2: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.12: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain B: D.225, S.249, G.251 Ligand excluded by PLIP CL.14: 1 residues within 4Å: Chain B: D.323 Ligand excluded by PLIP

3 x CS: CESIUM ION(Non-covalent)

CS.3: 3 residues within 4Å: Chain A: A.167, G.170, H.204 No protein-ligand interaction detected (PLIP) CS.15: 3 residues within 4Å: Chain B: T.66, T.69, T.71 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.71 CS.16: 6 residues within 4Å: Chain B: V.231, G.232, E.256, G.268, P.270, S.308 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:G.232

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

EDO.4: 4 residues within 4Å: Chain A: F.82, A.113, F.114, R.117 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.113 Water bridges: A:L.105, A:N.109 EDO.5: 7 residues within 4Å: Chain A: M.1, E.2, R.3, Y.4, E.5, D.124, N.147 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.2, A:E.2, A:Y.4, A:E.5, A:N.147 Water bridges: A:M.1, A:M.1 EDO.6: 4 residues within 4Å: Chain A: A.86, R.117, Q.120, V.121 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.117, A:R.117 Water bridges: A:V.121 EDO.17: 3 residues within 4Å: Chain B: I.319, G.320, R.321 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.320 Water bridges: B:R.321

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 6 residues within 4Å: Chain A: F.107, N.108, N.109, G.110 Chain B: R.275, V.276 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.275 Water bridges: B:V.276 PEG.18: 7 residues within 4Å: Chain B: N.6, Y.8, F.9, G.10, Q.312, Y.315, L.316 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.6, B:Y.8, B:G.10, B:Q.312

7 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.8: 6 residues within 4Å: Chain A: L.11, N.12, R.15, E.16, V.224, A.228 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.16 DMS.19: 4 residues within 4Å: Chain B: K.50, G.54, R.55, P.56 No protein-ligand interaction detected (PLIP) DMS.20: 2 residues within 4Å: Chain B: R.363, E.364 No protein-ligand interaction detected (PLIP) DMS.21: 2 residues within 4Å: Chain B: Q.36, Q.42 No protein-ligand interaction detected (PLIP) DMS.22: 2 residues within 4Å: Chain B: Y.8, G.10 1 PLIP interactions: 1 interactions with chain B pi-Cation interactions: B:Y.8 DMS.23: 5 residues within 4Å: Chain B: Q.42, F.45, A.46, L.49, M.207 No protein-ligand interaction detected (PLIP) DMS.24: 4 residues within 4Å: Chain B: T.3, L.4, L.5, N.6 2 PLIP interactions: 2 interactions with chain B Water bridges: B:T.3, B:T.3

1 x 0JO: 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid(Non-covalent)

0JO.9: 22 residues within 4Å: Chain B: A.85, H.86, K.87, T.110, G.111, A.112, G.113, A.114, H.115, T.190, C.230, V.231, G.232, G.233, G.234, S.235, N.236, G.303, L.304, E.350, S.377, G.378 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:A.85 Hydrogen bonds: B:K.87, B:T.110, B:G.111, B:A.112, B:G.113, B:A.114, B:H.115, B:G.232, B:G.233, B:G.234, B:S.235, B:S.235, B:N.236, B:N.236, B:S.377 Water bridges: B:T.190, B:T.190, B:A.237 Salt bridges: B:H.86, B:K.87, B:K.87 pi-Stacking: B:H.86

1 x SER: SERINE(Non-covalent)

SER.10: 6 residues within 4Å: Chain B: R.141, Q.142, S.299, I.300, A.302, D.305 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Ligand interactions Hydrogen bonds: B:R.141, B:Q.142, B:D.305 Water bridges: S.10, S.10

1 x BR: BROMIDE ION(Non-covalent)

BR.11: 2 residues within 4Å: Chain B: I.262, H.267 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hilario, E. et al., The aminoacrylate form of the beta-Q114A mutant Tryptophan Synthase at1.50 Angstrom resolution with cesium ion at the metal coordination site. To be Published

Release Date

2021-11-17

Peptides

Tryptophan synthase alpha chain: A
Tryptophan synthase beta chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Tryptophan synthase alpha chain

Tryptophan synthase beta chain

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