SMTL ID : 9dxb.1

Crystal structure of cobalt-incorporated human 2-aminoethanethiol (aka cysteamine) dioxygenase (ADO) variant C18S/C239S in complex with CP6-L8d-Gly-Ser

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.74 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: S.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

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

CL.2: 5 residues within 4Å: Chain A: Q.153, F.154, P.157, L.158, R.163 Ligand excluded by PLIP CL.3: 2 residues within 4Å: Chain A: A.8, R.16 Ligand excluded by PLIP

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: P.85, G.107, T.108, S.109, 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.5: 6 residues within 4Å: Chain A: N.68, I.69, A.70, R.72, M.89, P.265 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.70, A:R.72 Water bridges: A:E.262, A:P.263 GOL.6: 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:I.185 Water bridges: A:I.185, A:I.185, A:D.191 GOL.7: 4 residues within 4Å: Chain A: L.148, P.150, R.163, E.164 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.148, A:R.163 GOL.8: 4 residues within 4Å: Chain A: R.130, R.174, A.175, E.176 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.130, A:R.174, A:E.176 Water bridges: A:E.176

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-L8d-Gly-Ser: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

2-aminoethanethiol dioxygenase

CP6-L8d-Gly-Ser

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