SMTL ID : 3pr2.1

Tryptophan synthase indoline quinonoid structure with F9 inhibitor in alpha site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

hetero-2-2-mer

Ligands

2 x F9F: 2-({[4-(TRIFLUOROMETHOXY)PHENYL]SULFONYL}AMINO)ETHYL DIHYDROGEN PHOSPHATE(Non-covalent)

F9F.1: 19 residues within 4Å: Chain A: F.21, E.48, A.58, I.63, L.99, L.126, A.128, I.152, Y.174, L.176, T.182, G.183, F.211, G.212, I.231, S.232, G.233, S.234 Chain B: P.16 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.99, A:L.99, A:L.126, A:Y.174, A:T.182 Hydrogen bonds: A:R.178, A:G.183, A:F.211, A:G.212, A:G.233, A:S.234 Water bridges: A:F.211, A:I.213, A:A.235 pi-Stacking: A:F.211 F9F.6: 19 residues within 4Å: Chain C: F.21, E.48, A.58, I.63, L.99, L.126, A.128, I.152, Y.174, L.176, T.182, G.183, F.211, G.212, I.231, S.232, G.233, S.234 Chain D: P.16 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:L.99, C:L.99, C:L.126, C:Y.174, C:T.182 Hydrogen bonds: C:Y.174, C:R.178, C:G.183, C:F.211, C:G.212, C:G.233, C:S.234 Water bridges: C:F.211, C:I.213, C:A.235 pi-Stacking: C:F.211

2 x 7MN: (Z)-N-[(1E)-1-carboxy-2-(2,3-dihydro-1H-indol-1-yl)ethylidene]{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methanaminium(Non-covalent)

7MN.2: 27 residues within 4Å: Chain B: A.83, H.84, K.85, E.107, T.108, G.109, A.110, G.111, Q.112, H.113, L.164, G.187, T.188, C.228, V.229, G.230, G.231, G.232, S.233, N.234, G.301, L.302, F.304, A.346, E.348, S.375, G.376 29 PLIP interactions: 29 interactions with chain B Hydrophobic interactions: B:A.83, B:E.107, B:L.164, B:L.164, B:T.188, B:A.346, B:E.348 Hydrogen bonds: B:K.85, B:G.109, B:A.110, B:G.111, B:Q.112, B:H.113, B:T.188, B:G.230, B:G.231, B:G.232, B:S.233, B:N.234, B:N.234, B:S.375, B:S.375 Water bridges: B:G.232, B:A.235 Salt bridges: B:H.84, B:K.85, B:K.85 pi-Stacking: B:H.84, B:F.304 7MN.7: 27 residues within 4Å: Chain D: A.83, H.84, K.85, E.107, T.108, G.109, A.110, G.111, Q.112, H.113, L.164, G.187, T.188, C.228, V.229, G.230, G.231, G.232, S.233, N.234, G.301, L.302, F.304, A.346, E.348, S.375, G.376 30 PLIP interactions: 30 interactions with chain D Hydrophobic interactions: D:A.83, D:E.107, D:L.164, D:L.164, D:T.188, D:A.346, D:E.348 Hydrogen bonds: D:K.85, D:T.108, D:G.109, D:A.110, D:G.111, D:Q.112, D:H.113, D:T.188, D:G.230, D:G.231, D:G.232, D:S.233, D:N.234, D:N.234, D:S.375, D:S.375 Water bridges: D:G.232, D:A.235 Salt bridges: D:H.84, D:K.85, D:K.85 pi-Stacking: D:H.84, D:F.304

6 x CS: CESIUM ION(Non-covalent)

CS.3: 3 residues within 4Å: Chain B: T.64, T.67, T.69 No protein-ligand interaction detected (PLIP) CS.4: 6 residues within 4Å: Chain B: V.229, G.230, G.266, L.302, F.304, S.306 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:G.230, B:F.304, H2O.8 CS.5: 5 residues within 4Å: Chain B: G.52, P.54 Chain D: G.52, P.54 Ligands: CS.10 No protein-ligand interaction detected (PLIP) CS.8: 3 residues within 4Å: Chain D: T.64, T.67, T.69 No protein-ligand interaction detected (PLIP) CS.9: 6 residues within 4Å: Chain D: V.229, G.230, G.266, L.302, F.304, S.306 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:G.230, D:F.304, H2O.19 CS.10: 5 residues within 4Å: Chain B: G.52, P.54 Chain D: G.52, P.54 Ligands: CS.5 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lai, J. et al., X-ray and NMR Crystallography in an Enzyme Active Site: The Indoline Quinonoid Intermediate in Tryptophan Synthase. J.Am.Chem.Soc. (2011)

Release Date

2011-02-09

Peptides

Tryptophan synthase alpha chain: AC
Tryptophan synthase beta chain: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Tryptophan synthase alpha chain

Tryptophan synthase beta chain