SMTL ID : 9dxv.1

Crystal structure of cobalt-incorporated human 2-aminoethanethiol (aka cysteamine) dioxygenase (ADO) variant C18S/C239S in complex with CP6-L8K-Ser

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

hetero-1-1-mer

Ligands

1 x CO: COBALT (II) ION(Non-covalent)

CO.1: 4 residues within 4Å: Chain A: H.113, H.115, H.194 Chain B: K.9 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.113, A:H.115, A:H.194, H2O.2

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

CL.2: 4 residues within 4Å: Chain A: A.74, T.75, S.106, P.202 Ligand excluded by PLIP

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: P.85, T.108, S.109, P.111, D.256, F.257 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.109, A:S.109 Water bridges: A:D.256 GOL.4: 6 residues within 4Å: Chain A: C.133, S.173, Y.177, C.184, I.185, D.191 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.173, A:D.191 Water bridges: A:I.185, A:I.185, A:D.191 GOL.5: 5 residues within 4Å: Chain A: A.147, L.148, P.150, R.163, E.164 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.148, A:L.148, A:R.163, A:R.163, A:E.164 GOL.6: 6 residues within 4Å: Chain A: N.68, I.69, A.70, R.72, M.89, P.265 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.70, A:R.72 Water bridges: A:N.68 GOL.7: 1 residues within 4Å: Chain A: H.189 No protein-ligand interaction detected (PLIP) GOL.8: 3 residues within 4Å: Chain A: G.261, E.262, P.263 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.261 Water bridges: A:G.261, A:Y.264 GOL.13: 3 residues within 4Å: Chain B: Y.2, I.3 Ligands: GOL.14 No protein-ligand interaction detected (PLIP) GOL.14: 3 residues within 4Å: Chain B: I.3, K.5 Ligands: GOL.13 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:I.3, B:K.5, B:K.5 Water bridges: B:I.3, B:K.5

4 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.9: 3 residues within 4Å: Chain A: E.176, V.199, E.200 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.128, A:E.176 SCN.10: 4 residues within 4Å: Chain A: V.226, L.227, R.244 Ligands: SCN.12 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.227 SCN.11: 3 residues within 4Å: Chain A: G.117, P.188, H.189 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.117 SCN.12: 3 residues within 4Å: Chain A: V.226, R.244 Ligands: SCN.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.244

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jiramongkol, Y. et al., An mRNA-display derived cyclic peptide scaffold reveals the substrate binding interactions of an N-terminal cysteine oxidase. Nat Commun (2025)

Release Date

2025-06-04

Peptides

2-aminoethanethiol dioxygenase: A
CP6-L8K-Ser: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

2-aminoethanethiol dioxygenase

CP6-L8K-Ser

Related Entries With Identical Sequence