SMTL ID : 8pte.1

Polyoxidovanadate interaction with proteins: crystal structure of lysozyme bound to octadecavanadate ion (structure B)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

NA.1: 4 residues within 4Å: Chain A: S.60, C.64, S.72, R.73 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.72, A:R.73 NA.7: 4 residues within 4Å: Chain B: S.60, C.64, S.72, R.73 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.72, B:S.72

2 x JQJ: Polyoxidovanadate complex

JQJ.2: 17 residues within 4Å: Chain A: K.1, F.3, E.7, A.10, A.11, R.14, H.15, S.86, D.87, I.88, T.89 Chain B: K.1, E.7, R.14 Ligands: NO3.6, JQJ.8, NO3.12 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.1, A:E.7, A:E.7, A:A.11, A:R.14, A:D.87, A:I.88, A:T.89, B:K.1 Water bridges: A:A.11, A:A.11, A:S.86, A:T.89, B:K.1 JQJ.8: 17 residues within 4Å: Chain A: K.1, E.7, R.14 Chain B: K.1, F.3, E.7, A.10, A.11, R.14, H.15, S.86, D.87, I.88, T.89 Ligands: JQJ.2, NO3.6, NO3.12 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.1, B:E.7, B:A.11, B:R.14, B:H.15, B:D.87, B:I.88, B:T.89, B:T.89, A:K.1 Water bridges: B:A.11, B:A.11, B:S.86

2 x H1W: pentakis(oxidanyl)vanadium(Non-covalent)

H1W.3: 8 residues within 4Å: Chain A: E.35, N.46, D.52, L.56, Q.57, N.59, A.107, V.109 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:E.35, A:E.35, A:N.46, A:A.107, A:V.109 Water bridges: A:Q.57, A:N.59, A:N.59, A:A.107 H1W.9: 8 residues within 4Å: Chain B: E.35, N.46, D.52, L.56, Q.57, N.59, A.107, V.109 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:E.35, B:E.35, B:N.46, B:A.107, B:V.109 Water bridges: B:E.35, B:E.35, B:Q.57, B:N.59, B:N.59, B:A.107

6 x NO3: NITRATE ION(Non-functional Binders)

NO3.4: 4 residues within 4Å: Chain A: R.5, K.33, F.38, W.123 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.33 Water bridges: A:R.5 NO3.5: 3 residues within 4Å: Chain A: S.24, N.27, V.120 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.24, A:S.24, A:N.27 Water bridges: A:T.118, A:T.118, A:V.120, A:V.120 NO3.6: 3 residues within 4Å: Ligands: JQJ.2, JQJ.8, NO3.12 No protein-ligand interaction detected (PLIP) NO3.10: 4 residues within 4Å: Chain B: R.5, K.33, F.38, W.123 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.33 Water bridges: B:R.5 NO3.11: 3 residues within 4Å: Chain B: S.24, N.27, V.120 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.24, B:S.24, B:N.27 Water bridges: B:T.118, B:T.118, B:V.120, B:V.120 NO3.12: 3 residues within 4Å: Ligands: JQJ.2, NO3.6, JQJ.8 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ferraro, G. et al., Stabilization and Binding of [V 4 O 12 ] 4- and Unprecedented [V 20 O 54 (NO 3 )] n- to Lysozyme upon Loss of Ligands and Oxidation of the Potential Drug V IV O(acetylacetonato) 2. Angew.Chem.Int.Ed.Engl. (2023)

Release Date

2024-01-10

Peptides

Lysozyme C: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
AAA

Lysozyme C

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