SMTL ID : 7pgx.1

Structure of dark-adapted AsLOV2 wild type

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.00 Å

Oligo State

monomer

Ligands

1 x CA: CALCIUM ION(Non-covalent)

CA.1: 2 residues within 4Å: Chain A: D.115, G.116 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.115, H2O.7

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

CL.2: 3 residues within 4Å: Chain A: V.120, R.121, A.124 Ligand excluded by PLIP

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 2 residues within 4Å: Chain A: F.3, L.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.4 Water bridges: A:F.3 GOL.4: 5 residues within 4Å: Chain A: P.56, E.57, T.58, D.59, R.60 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.57, A:R.60 Water bridges: A:A.61 GOL.5: 4 residues within 4Å: Chain A: E.75, T.77, H.95, V.129 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.75, A:T.77 Water bridges: A:H.95 GOL.6: 3 residues within 4Å: Chain A: R.64, R.67, D.68 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.64, A:R.67, A:D.68 Water bridges: A:D.68 GOL.7: 4 residues within 4Å: Chain A: N.14, S.33, L.37, D.115 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.14, A:N.14 Water bridges: A:D.115 GOL.8: 4 residues within 4Å: Chain A: F.3, E.43, L.46 Ligands: GOL.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.43, A:L.46 GOL.9: 5 residues within 4Å: Chain A: T.77, V.78, Q.79, H.119, E.125 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.77, A:Q.79, A:H.119 Water bridges: A:Q.79 GOL.10: 2 residues within 4Å: Chain A: E.137, E.141 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.141 Water bridges: A:E.137, A:E.137 GOL.11: 4 residues within 4Å: Chain A: P.20, R.21, Q.73, V.106 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.73, A:V.106 Water bridges: A:V.106 GOL.12: 3 residues within 4Å: Chain A: P.23, G.47 Ligands: GOL.8 1 PLIP interactions: 1 interactions with chain A Water bridges: A:P.23

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.13: 7 residues within 4Å: Chain A: G.1, E.2, F.3, L.4, L.35, S.41, R.42 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.1, A:R.42 Water bridges: A:E.2, A:A.5 PEG.14: 4 residues within 4Å: Chain A: D.101, D.105, V.106, Q.107 No protein-ligand interaction detected (PLIP)

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.15: 5 residues within 4Å: Chain A: L.35, Q.36, E.39, Y.40, S.41 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.40 EDO.16: 1 residues within 4Å: Chain A: L.131 No protein-ligand interaction detected (PLIP)

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.17: 5 residues within 4Å: Chain A: K.13, N.14, V.112, Q.113, L.114 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.112 Hydrogen bonds: A:N.14 Water bridges: A:N.14

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.18: 21 residues within 4Å: Chain A: V.16, T.18, N.25, N.49, C.50, R.51, L.53, Q.54, V.63, I.66, R.67, I.70, L.80, N.82, N.92, F.94, L.96, F.109, I.110, G.111, Q.113 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:V.16, A:T.18, A:F.94, A:L.96 Hydrogen bonds: A:N.49, A:C.50, A:Q.54, A:N.82, A:N.82, A:N.92, A:Q.113 Water bridges: A:R.51, A:R.51, A:R.51, A:R.60, A:R.60 Salt bridges: A:R.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dietler, J. et al., Signal transduction in light-oxygen-voltage receptors lacking the active-site glutamine. Nat Commun (2022)

Release Date

2022-05-11

Peptides

NPH1-1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

NPH1-1

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