SMTL ID : 7zab.1

Sam68

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.46 Å

Oligo State

homo-dimer

Ligands

2 x IOD: IODIDE ION(Non-functional Binders)

IOD.1: 3 residues within 4Å: Chain A: Y.25, P.26, K.27 Ligand excluded by PLIP IOD.15: 3 residues within 4Å: Chain B: Y.25, P.26, K.27 Ligand excluded by PLIP

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

CL.2: 2 residues within 4Å: Chain A: K.10, N.11 Ligand excluded by PLIP CL.3: 1 residues within 4Å: Chain A: N.2 Ligand excluded by PLIP CL.4: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain B: K.10, N.11 Ligand excluded by PLIP CL.17: 1 residues within 4Å: Chain B: N.2 Ligand excluded by PLIP CL.18: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

2 x LI: LITHIUM ION(Non-covalent)

LI.5: 6 residues within 4Å: Chain A: V.22, Y.25, P.26, F.28, F.30 Ligands: EDO.11 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:Y.25, A:F.28 LI.19: 6 residues within 4Å: Chain B: V.22, Y.25, P.26, F.28, F.30 Ligands: EDO.25 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:Y.25, B:F.28

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 3 residues within 4Å: Chain A: K.13, K.15 Ligands: DMS.14 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.13, A:K.13, A:K.15 GOL.20: 3 residues within 4Å: Chain B: K.13, K.15 Ligands: DMS.28 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.13, B:K.13, B:K.15

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.7: 6 residues within 4Å: Chain A: L.6, P.94, P.95, C.96, E.97 Chain B: K.110 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.94, B:K.110, B:K.110 Hydrogen bonds: A:P.94, A:C.96, A:E.97 MPD.21: 6 residues within 4Å: Chain A: K.110 Chain B: L.6, P.94, P.95, C.96, E.97 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:K.110, A:K.110, B:P.94 Hydrogen bonds: B:P.94, B:C.96, B:E.97

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

EDO.8: 1 residues within 4Å: Chain A: G.73 No protein-ligand interaction detected (PLIP) EDO.9: 2 residues within 4Å: Chain A: K.33, F.112 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.33 EDO.10: 1 residues within 4Å: Chain A: R.17 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.17 EDO.11: 6 residues within 4Å: Chain A: V.22, F.28, N.29, F.30, V.31 Ligands: LI.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.29, A:F.30, A:V.31 EDO.12: 6 residues within 4Å: Chain A: Y.3, L.4, D.5, S.8, K.10, P.95 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.5, A:S.8, A:K.10 EDO.13: 4 residues within 4Å: Chain A: I.42, I.53, S.54, V.55 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.55, A:V.55 EDO.22: 1 residues within 4Å: Chain B: G.73 No protein-ligand interaction detected (PLIP) EDO.23: 2 residues within 4Å: Chain B: K.33, F.112 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.33 EDO.24: 1 residues within 4Å: Chain B: R.17 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.17 EDO.25: 6 residues within 4Å: Chain B: V.22, F.28, N.29, F.30, V.31 Ligands: LI.19 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.29, B:F.30, B:V.31 EDO.26: 6 residues within 4Å: Chain B: Y.3, L.4, D.5, S.8, K.10, P.95 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.5, B:S.8, B:K.10 EDO.27: 4 residues within 4Å: Chain B: I.42, I.53, S.54, V.55 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.55, B:V.55

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.14: 5 residues within 4Å: Chain A: K.15, E.90, V.91, F.92 Ligands: GOL.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.15 DMS.28: 5 residues within 4Å: Chain B: K.15, E.90, V.91, F.92 Ligands: GOL.20 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.15

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nadal, M. et al., Structure and function analysis of Sam68 and hnRNP A1 synergy in the exclusion of exon 7 from SMN2 transcripts. Protein Sci. (2023)

Release Date

2023-02-01

Peptides

Isoform 2 of KH domain-containing, RNA-binding, signal transduction-associated protein 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
AAA

Isoform 2 of KH domain-containing, RNA-binding, signal transduction-associated protein 1

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