SMTL ID : 8a9s.1 (1 other biounit)

Crystal structure of Ca2+-discharged obelin in complex with coelenteramine-v

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x LK9: 3-azanyl-2-(phenylmethyl)benzo[f]quinoxalin-8-ol(Non-covalent)

LK9.1: 19 residues within 4Å: Chain A: H.22, M.25, F.28, L.29, A.46, F.72, F.88, W.92, I.111, W.114, G.115, V.118, W.135, Y.138, S.142, I.144, H.175, W.179, Y.190 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:M.25, A:F.72, A:W.92, A:W.114, A:V.118, A:W.179, A:W.179 Hydrogen bonds: A:H.22, A:W.92, A:Y.138 pi-Cation interactions: A:H.175

1 x NA: SODIUM ION(Non-functional Binders)

NA.2: 5 residues within 4Å: Chain A: D.30, N.32, N.34, K.36, I.37 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.30, A:N.32, A:N.34, A:K.36 Water bridges: A:D.30, A:N.34

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

DMS.3: 3 residues within 4Å: Chain A: L.160, D.161, N.162 No protein-ligand interaction detected (PLIP) DMS.4: 8 residues within 4Å: Chain A: H.24, M.25, F.28, G.143, I.144, P.146, G.193, V.194 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.24 DMS.5: 6 residues within 4Å: Chain A: L.54, E.55, I.121, F.122, K.124, E.134 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.124

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Natashin, P.V. et al., Crystal structure of semi-synthetic obelin-v after calcium induced bioluminescence implies coelenteramine as the main reaction product. Sci Rep (2022)

Release Date

2022-10-19

Peptides

Obelin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Obelin

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