SMTL ID : 7zvx.2 (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

6 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: K.56, S.57, L.59, E.64 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:K.56, A:L.59 CA.2: 4 residues within 4Å: Chain A: M.86, G.88, G.90, 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.3: 5 residues within 4Å: Chain A: G.170, R.173, K.174, G.175, E.215 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:G.170, A:R.173, A:G.175, A:E.215 CA.4: 3 residues within 4Å: Chain A: R.213, K.217, E.221 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.221 CA.5: 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.6: 2 residues within 4Å: Chain A: T.91, D.92 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.91

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

EDO.7: 5 residues within 4Å: Chain A: T.29, R.31, S.264, Y.301, L.302 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.264 EDO.8: 7 residues within 4Å: Chain A: N.33, R.36, G.69, L.70, K.72, P.74, A.261 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.33, A:R.36, A:L.70 Water bridges: A:S.262, A:S.262 EDO.9: 8 residues within 4Å: Chain A: C.101, S.102, R.103, R.147, L.227, C.230, K.234 Ligands: EDO.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.147, A:R.147, A:K.234, A:K.234 EDO.10: 6 residues within 4Å: Chain A: T.104, N.105, Q.106, E.149, V.190 Ligands: EDO.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.105, A:Q.106, A:Q.106 EDO.11: 8 residues within 4Å: Chain A: V.190, Q.194, C.230, I.231, Q.232, N.233, K.234, P.235 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.234, A:K.234, A:K.234 EDO.12: 8 residues within 4Å: Chain A: D.244, S.245, M.246, K.247, G.248, K.249, G.250, R.252 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.247, A:G.248 Water bridges: A:K.249, A:T.251

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
B

Annexin A2

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