SMTL ID : 1nu4.3 (6 other biounits)

U1A RNA binding domain at 1.8 angstrom resolution reveals a pre-organized C-terminal helix

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-hexamer

Ligands

15 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: R.69 Chain C: R.69 Chain E: R.69 Ligands: MG.18, MG.35 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: A:R.69, C:R.69, E:R.69, H2O.1, H2O.4, H2O.8 MG.2: 1 residues within 4Å: Chain A: D.41 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.41, H2O.2, H2O.2 MG.9: 5 residues within 4Å: Chain B: R.69 Chain D: R.69 Chain F: R.69 Ligands: MG.26, MG.43 6 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D, 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: B:R.69, D:R.69, F:R.69, H2O.3, H2O.7, H2O.10 MG.10: 1 residues within 4Å: Chain B: D.41 No protein-ligand interaction detected (PLIP) MG.11: 5 residues within 4Å: Chain B: K.21, K.22, D.23, R.46 Ligands: MLA.15 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.23 MG.18: 5 residues within 4Å: Chain A: R.69 Chain C: R.69 Chain E: R.69 Ligands: MG.1, MG.35 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: A:R.69, C:R.69, E:R.69, H2O.1, H2O.4, H2O.8 MG.19: 1 residues within 4Å: Chain C: D.41 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.41, H2O.6, H2O.6 MG.26: 5 residues within 4Å: Chain B: R.69 Chain D: R.69 Chain F: R.69 Ligands: MG.9, MG.43 6 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D, 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: B:R.69, D:R.69, F:R.69, H2O.3, H2O.7, H2O.10 MG.27: 1 residues within 4Å: Chain D: D.41 No protein-ligand interaction detected (PLIP) MG.28: 5 residues within 4Å: Chain D: K.21, K.22, D.23, R.46 Ligands: MLA.32 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.23 MG.35: 5 residues within 4Å: Chain A: R.69 Chain C: R.69 Chain E: R.69 Ligands: MG.1, MG.18 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: A:R.69, C:R.69, E:R.69, H2O.1, H2O.4, H2O.8 MG.36: 1 residues within 4Å: Chain E: D.41 3 PLIP interactions: 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.41, H2O.10, H2O.10 MG.43: 5 residues within 4Å: Chain B: R.69 Chain D: R.69 Chain F: R.69 Ligands: MG.9, MG.26 6 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D, 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: B:R.69, D:R.69, F:R.69, H2O.3, H2O.7, H2O.10 MG.44: 1 residues within 4Å: Chain F: D.41 No protein-ligand interaction detected (PLIP) MG.45: 5 residues within 4Å: Chain F: K.21, K.22, D.23, R.46 Ligands: MLA.49 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.23

36 x MLA: MALONIC ACID(Non-covalent)

MLA.3: 4 residues within 4Å: Chain A: Y.12, F.55, A.86, K.87 Ligand excluded by PLIP MLA.4: 7 residues within 4Å: Chain A: V.61, S.62, T.65 Chain D: V.61, S.62, T.65, R.69 Ligand excluded by PLIP MLA.5: 6 residues within 4Å: Chain A: R.6, Y.85 Chain C: I.32, R.35, M.71, F.74 Ligand excluded by PLIP MLA.6: 6 residues within 4Å: Chain A: K.26, H.30, I.39, L.40, D.41, I.42 Ligand excluded by PLIP MLA.7: 1 residues within 4Å: Chain A: A.94 Ligand excluded by PLIP MLA.8: 4 residues within 4Å: Chain A: K.22, S.45, R.46, S.47 Ligand excluded by PLIP MLA.12: 8 residues within 4Å: Chain B: T.5, L.68, R.69, Y.85 Chain F: I.32, R.35, M.71, F.74 Ligand excluded by PLIP MLA.13: 4 residues within 4Å: Chain B: Y.12, F.55, A.86, K.87 Ligand excluded by PLIP MLA.14: 7 residues within 4Å: Chain B: N.8, H.9, T.10, T.88, D.89, S.90, D.91 Ligand excluded by PLIP MLA.15: 4 residues within 4Å: Chain B: K.21, K.22, R.46 Ligands: MG.11 Ligand excluded by PLIP MLA.16: 4 residues within 4Å: Chain B: N.15, D.78, K.79, P.80 Ligand excluded by PLIP MLA.17: 5 residues within 4Å: Chain B: S.28, F.74, P.75, F.76, Y.77 Ligand excluded by PLIP MLA.20: 4 residues within 4Å: Chain C: Y.12, F.55, A.86, K.87 Ligand excluded by PLIP MLA.21: 7 residues within 4Å: Chain C: V.61, S.62, T.65 Chain F: V.61, S.62, T.65, R.69 Ligand excluded by PLIP MLA.22: 6 residues within 4Å: Chain C: R.6, Y.85 Chain E: I.32, R.35, M.71, F.74 Ligand excluded by PLIP MLA.23: 6 residues within 4Å: Chain C: K.26, H.30, I.39, L.40, D.41, I.42 Ligand excluded by PLIP MLA.24: 1 residues within 4Å: Chain C: A.94 Ligand excluded by PLIP MLA.25: 4 residues within 4Å: Chain C: K.22, S.45, R.46, S.47 Ligand excluded by PLIP MLA.29: 8 residues within 4Å: Chain B: I.32, R.35, M.71, F.74 Chain D: T.5, L.68, R.69, Y.85 Ligand excluded by PLIP MLA.30: 4 residues within 4Å: Chain D: Y.12, F.55, A.86, K.87 Ligand excluded by PLIP MLA.31: 7 residues within 4Å: Chain D: N.8, H.9, T.10, T.88, D.89, S.90, D.91 Ligand excluded by PLIP MLA.32: 4 residues within 4Å: Chain D: K.21, K.22, R.46 Ligands: MG.28 Ligand excluded by PLIP MLA.33: 4 residues within 4Å: Chain D: N.15, D.78, K.79, P.80 Ligand excluded by PLIP MLA.34: 5 residues within 4Å: Chain D: S.28, F.74, P.75, F.76, Y.77 Ligand excluded by PLIP MLA.37: 4 residues within 4Å: Chain E: Y.12, F.55, A.86, K.87 Ligand excluded by PLIP MLA.38: 7 residues within 4Å: Chain B: V.61, S.62, T.65, R.69 Chain E: V.61, S.62, T.65 Ligand excluded by PLIP MLA.39: 6 residues within 4Å: Chain A: I.32, R.35, M.71, F.74 Chain E: R.6, Y.85 Ligand excluded by PLIP MLA.40: 6 residues within 4Å: Chain E: K.26, H.30, I.39, L.40, D.41, I.42 Ligand excluded by PLIP MLA.41: 1 residues within 4Å: Chain E: A.94 Ligand excluded by PLIP MLA.42: 4 residues within 4Å: Chain E: K.22, S.45, R.46, S.47 Ligand excluded by PLIP MLA.46: 8 residues within 4Å: Chain D: I.32, R.35, M.71, F.74 Chain F: T.5, L.68, R.69, Y.85 Ligand excluded by PLIP MLA.47: 4 residues within 4Å: Chain F: Y.12, F.55, A.86, K.87 Ligand excluded by PLIP MLA.48: 7 residues within 4Å: Chain F: N.8, H.9, T.10, T.88, D.89, S.90, D.91 Ligand excluded by PLIP MLA.49: 4 residues within 4Å: Chain F: K.21, K.22, R.46 Ligands: MG.45 Ligand excluded by PLIP MLA.50: 4 residues within 4Å: Chain F: N.15, D.78, K.79, P.80 Ligand excluded by PLIP MLA.51: 5 residues within 4Å: Chain F: S.28, F.74, P.75, F.76, Y.77 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rupert, P.B. et al., U1A RNA-binding domain at 1.8 A resolution. Acta Crystallogr.,Sect.D (2003)

Release Date

2003-02-14

Peptides

U1A RNA binding domain: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

U1A RNA binding domain

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