SMTL ID : 7zvx.1 (1 other biounit)

Crystal structure of human Annexin A2 in complex with full phosphorothioate 5-10 2'-methoxyethyl DNA gapmer antisense oligonucleotide solved at 2.4 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

5 x CA: CALCIUM ION(Non-covalent)

CA.1: 7 residues within 4Å: Chain A: M.86, K.87, G.88, L.89, G.90, T.91, D.130 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:M.86, A:G.88, A:G.90, A:D.130 CA.2: 4 residues within 4Å: Chain A: M.246, G.248, G.250, D.290 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:M.246, A:G.248, A:G.250, A:D.290, A:D.290 CA.3: 3 residues within 4Å: Chain A: K.56, L.59, E.64 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:K.56, A:L.59, H2O.4 CA.4: 1 residues within 4Å: Chain A: R.213 No protein-ligand interaction detected (PLIP) CA.5: 3 residues within 4Å: Chain A: R.173, G.175, E.215 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.215

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

EDO.6: 6 residues within 4Å: Chain A: T.29, R.31, S.264, E.265, Y.301, L.302 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.264 Water bridges: A:R.36 EDO.7: 7 residues within 4Å: Chain A: N.33, R.36, G.69, L.70, K.72, Y.77, A.261 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.36, A:G.69 Water bridges: A:A.261, A:S.262 EDO.8: 9 residues within 4Å: Chain A: C.101, R.103, R.147, V.190, L.227, C.230, I.231, K.234 Ligands: EDO.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.147, A:R.147, A:K.234, A:K.234 EDO.9: 7 residues within 4Å: Chain A: T.104, N.105, Q.106, R.147, E.149, V.190 Ligands: EDO.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.105, A:Q.106 EDO.10: 6 residues within 4Å: Chain A: A.141, K.144, G.145, R.146, R.147, T.186 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.146 EDO.11: 2 residues within 4Å: Chain A: Y.243, K.247 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.243 EDO.12: 8 residues within 4Å: Chain A: D.244, S.245, M.246, K.247, G.248, K.249, G.250, R.252 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.247, A:G.248

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hyjek-Skladanowska, M. et al., Structures of annexin A2-PS DNA complexes show dominance of hydrophobic interactions in phosphorothioate binding. Nucleic Acids Res. (2023)

Release Date

2022-09-14

Peptides

Annexin A2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Annexin A2

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