SMTL ID : 7zvn.1

Crystal structure of human Annexin A2 in complex with full phosphorothioate 5-10 2'-methoxyethyl DNA gapmer antisense oligonucleotide solved at 1.87 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

monomer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: C.101, S.102, R.103, T.104, R.147, V.190, L.227, C.230, K.234 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.147, A:K.234 Water bridges: A:R.103, A:R.103, A:N.105, A:N.105, A:R.147 GOL.2: 7 residues within 4Å: Chain A: A.148, E.149, G.151, D.155, R.188, S.189, H.192 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.149, A:G.151, A:S.189, A:S.189, A:H.192 Water bridges: A:D.155, A:D.155 GOL.3: 5 residues within 4Å: Chain A: K.201, S.202, Y.203, S.204, P.205 No protein-ligand interaction detected (PLIP) GOL.4: 7 residues within 4Å: Chain A: R.263, S.264, E.265, V.266, D.267, M.268, L.269 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.264, A:M.268, A:L.269 GOL.5: 9 residues within 4Å: Chain A: D.244, S.245, M.246, K.247, G.248, K.249, G.250, T.251, R.252 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.247, A:G.248, A:K.249, A:R.252 GOL.6: 6 residues within 4Å: Chain A: P.74, D.78, R.103, E.107, S.262, R.263 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.263, A:R.263 Water bridges: A:P.74, A:D.78 GOL.7: 4 residues within 4Å: Chain A: R.164, Y.167, D.168, Y.203 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.164, A:R.164 Water bridges: A:K.172, A:K.172 GOL.8: 5 residues within 4Å: Chain A: V.153, I.154, D.155, Y.156, E.157 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.156, A:E.157 Water bridges: A:E.157

7 x CA: CALCIUM ION(Non-covalent)

CA.9: 3 residues within 4Å: Chain A: G.18, V.19, E.21 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.18, A:E.21, A:E.21, H2O.7, H2O.10 CA.10: 4 residues within 4Å: Chain A: M.86, G.88, G.90, D.130 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:M.86, A:G.88, A:G.90, H2O.7, H2O.7 CA.11: 4 residues within 4Å: Chain A: G.170, R.173, G.175, E.215 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.170, A:R.173, A:G.175, H2O.5, H2O.10 CA.12: 3 residues within 4Å: Chain A: K.56, L.59, E.64 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:K.56, A:L.59, A:E.64, H2O.9, H2O.10 CA.13: 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.14: 2 residues within 4Å: Chain A: T.91, E.93 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.93, H2O.1, H2O.7, H2O.10, H2O.11 CA.15: 3 residues within 4Å: Chain A: R.213, V.216, E.221 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:R.213, A:V.216, A:E.221, H2O.7, H2O.8

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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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