SMTL ID : 8vyy.1

The crystal structure of MarE in complex with its native substrate, beta-methyl-L-tryptophan

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-tetramer

Ligands

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 21 residues within 4Å: Chain A: F.53, T.56, H.57, T.60, L.107, T.128, G.129, L.130, S.132, Y.135, W.199, K.200, H.203, M.206, V.207, L.211, S.238, L.242, R.245 Chain B: Y.26 Ligands: 78U.2 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:F.53, A:T.60, A:L.130, A:Y.135, A:W.199, A:V.207, A:L.242, A:L.242 Hydrogen bonds: A:T.128, A:T.128, A:Y.135 Salt bridges: A:K.200, A:R.245 Metal complexes: A:H.203 HEM.3: 19 residues within 4Å: Chain B: F.53, T.56, H.57, T.60, L.107, L.116, T.128, G.129, L.130, Y.135, W.199, H.203, M.206, V.207, Q.210, S.238, L.242, R.245 Ligands: 78U.4 11 PLIP interactions: 11 interactions with chain B, Hydrophobic interactions: B:F.53, B:T.60, B:L.116, B:Y.135, B:W.199, B:V.207, B:Q.210, B:L.242 Salt bridges: B:K.200, B:R.245 Metal complexes: B:H.203 HEM.5: 21 residues within 4Å: Chain C: F.53, T.56, H.57, T.60, L.107, T.128, G.129, L.130, S.132, Y.135, W.199, K.200, H.203, M.206, V.207, L.211, S.238, L.242, R.245 Chain D: Y.26 Ligands: 78U.6 12 PLIP interactions: 12 interactions with chain C, Hydrophobic interactions: C:F.53, C:T.60, C:L.130, C:Y.135, C:W.199, C:V.207, C:L.242, C:L.242 Hydrogen bonds: C:T.128 Salt bridges: C:K.200, C:R.245 Metal complexes: C:H.203 HEM.7: 19 residues within 4Å: Chain D: F.53, T.56, H.57, T.60, L.107, L.116, T.128, G.129, L.130, Y.135, W.199, H.203, M.206, V.207, Q.210, S.238, L.242, R.245 Ligands: 78U.8 13 PLIP interactions: 13 interactions with chain D, Hydrophobic interactions: D:F.53, D:T.60, D:L.116, D:Y.135, D:W.199, D:V.207, D:Q.210, D:L.242 Hydrogen bonds: D:T.128, D:Y.135 Salt bridges: D:K.200, D:R.245 Metal complexes: D:H.203

4 x 78U: (betaS)-beta-methyl-L-tryptophan(Non-covalent)

78U.2: 10 residues within 4Å: Chain A: F.53, H.57, R.120, L.123, A.127, T.128, G.129 Chain B: Y.26, V.29 Ligands: HEM.1 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.123, A:A.127, B:Y.26, B:V.29 Hydrogen bonds: A:H.57 Salt bridges: A:R.120 pi-Stacking: A:F.53 78U.4: 11 residues within 4Å: Chain A: Y.26, L.30 Chain B: F.53, H.57, R.120, L.123, A.127, T.128, G.129, L.211 Ligands: HEM.3 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.123, B:A.127, A:Y.26, A:L.30 Hydrogen bonds: B:H.57 Salt bridges: B:R.120 pi-Stacking: B:F.53 78U.6: 10 residues within 4Å: Chain C: F.53, H.57, R.120, L.123, A.127, T.128, G.129 Chain D: Y.26, V.29 Ligands: HEM.5 7 PLIP interactions: 2 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:Y.26, D:V.29, C:L.123, C:A.127 Hydrogen bonds: C:H.57 Salt bridges: C:R.120 pi-Stacking: C:F.53 78U.8: 11 residues within 4Å: Chain C: Y.26, L.30 Chain D: F.53, H.57, R.120, L.123, A.127, T.128, G.129, L.211 Ligands: HEM.7 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:L.123, D:A.127, C:Y.26, C:L.30 Hydrogen bonds: D:H.57 Salt bridges: D:R.120 pi-Stacking: D:F.53

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shin, I. et al., Structural insights into 2-oxindole-forming monooxygenase MarE: Divergent architecture and substrate positioning versus tryptophan dioxygenases. J.Biol.Chem. (2025)

Release Date

2025-04-02

Peptides

Tryptophan 2,3-dioxygenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Tryptophan 2,3-dioxygenase