SMTL ID : 7z8a.1

Sam68

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

homo-dimer

Ligands

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

NO3.1: 4 residues within 4Å: Chain A: Y.23, P.24, K.25, F.26 Ligand excluded by PLIP NO3.2: 5 residues within 4Å: Chain A: I.18, P.19, V.20, K.21, Q.22 Ligand excluded by PLIP NO3.3: 6 residues within 4Å: Chain A: R.15, L.54, H.78, M.81, F.86 Ligands: PGO.17 Ligand excluded by PLIP NO3.4: 3 residues within 4Å: Chain A: N.27, G.30, K.31 Ligand excluded by PLIP NO3.5: 4 residues within 4Å: Chain A: P.24, K.25, F.26 Ligands: EDO.12 Ligand excluded by PLIP NO3.6: 2 residues within 4Å: Chain A: L.4, F.5 Ligand excluded by PLIP NO3.7: 4 residues within 4Å: Chain A: V.20, K.56, D.82, L.83 Ligand excluded by PLIP NO3.8: 6 residues within 4Å: Chain A: L.4, P.92, P.93, C.94, E.95 Chain B: K.108 Ligand excluded by PLIP NO3.18: 4 residues within 4Å: Chain B: Y.23, P.24, K.25, F.26 Ligand excluded by PLIP NO3.19: 5 residues within 4Å: Chain B: I.18, P.19, V.20, K.21, Q.22 Ligand excluded by PLIP NO3.20: 6 residues within 4Å: Chain B: R.15, L.54, H.78, M.81, F.86 Ligands: PGO.34 Ligand excluded by PLIP NO3.21: 3 residues within 4Å: Chain B: N.27, G.30, K.31 Ligand excluded by PLIP NO3.22: 4 residues within 4Å: Chain B: P.24, K.25, F.26 Ligands: EDO.29 Ligand excluded by PLIP NO3.23: 2 residues within 4Å: Chain B: L.4, F.5 Ligand excluded by PLIP NO3.24: 4 residues within 4Å: Chain B: V.20, K.56, D.82, L.83 Ligand excluded by PLIP NO3.25: 6 residues within 4Å: Chain A: K.108 Chain B: L.4, P.92, P.93, C.94, E.95 Ligand excluded by PLIP

2 x LI: LITHIUM ION(Non-covalent)

LI.9: 2 residues within 4Å: Chain A: Y.23, D.114 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.114, H2O.1, H2O.2 LI.26: 2 residues within 4Å: Chain B: Y.23, D.114 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.114, H2O.3, H2O.4

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

EDO.10: 3 residues within 4Å: Chain A: S.6, H.7, K.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.7, A:H.7 EDO.11: 4 residues within 4Å: Chain A: K.50, E.88, V.89, F.90 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.50 Water bridges: A:K.13, A:G.48, A:E.88, A:V.89, A:F.90 EDO.12: 7 residues within 4Å: Chain A: V.20, F.26, N.27, F.28, V.29, L.83 Ligands: NO3.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.27, A:F.28, A:V.29 Water bridges: A:F.26 EDO.13: 6 residues within 4Å: Chain A: L.68, R.69, G.72, D.73, Y.76, N.80 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.72, A:D.73, A:N.80 Water bridges: A:D.73 EDO.14: 3 residues within 4Å: Chain A: G.48, E.95, L.99 3 PLIP interactions: 3 interactions with chain A Water bridges: A:G.48, A:F.90, A:E.95 EDO.27: 3 residues within 4Å: Chain B: S.6, H.7, K.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.7, B:H.7 EDO.28: 4 residues within 4Å: Chain B: K.50, E.88, V.89, F.90 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.50 Water bridges: B:K.13, B:G.48, B:E.88, B:V.89, B:F.90 EDO.29: 7 residues within 4Å: Chain B: V.20, F.26, N.27, F.28, V.29, L.83 Ligands: NO3.22 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.27, B:F.28, B:V.29 Water bridges: B:F.26 EDO.30: 6 residues within 4Å: Chain B: L.68, R.69, G.72, D.73, Y.76, N.80 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.72, B:D.73, B:N.80 Water bridges: B:D.73 EDO.31: 3 residues within 4Å: Chain B: G.48, E.95, L.99 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.95 Water bridges: B:G.48, B:F.90, B:E.95

6 x PGO: S-1,2-PROPANEDIOL(Non-covalent)

PGO.15: 2 residues within 4Å: Chain A: K.31, K.109 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.31 PGO.16: 7 residues within 4Å: Chain A: L.2, D.3, S.6, K.8, N.9, M.10, P.93 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.93 Hydrogen bonds: A:D.3, A:N.9 PGO.17: 3 residues within 4Å: Chain A: R.15, M.81 Ligands: NO3.3 No protein-ligand interaction detected (PLIP) PGO.32: 2 residues within 4Å: Chain B: K.31, K.109 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.31 PGO.33: 7 residues within 4Å: Chain B: L.2, D.3, S.6, K.8, N.9, M.10, P.93 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.93 Hydrogen bonds: B:D.3, B:N.9 PGO.34: 3 residues within 4Å: Chain B: R.15, M.81 Ligands: NO3.20 No protein-ligand interaction detected (PLIP)

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

KHDR1 protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
AAA

KHDR1 protein