SMTL ID : 4v4f.1 (3 other biounits)

The structure of the trp RNA-binding attenuation protein (TRAP) bound to a RNA molecule containing UAGAU repeats

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-11-mer

Ligands

11 x A- G- A: 5'-R(*UP*AP*GP*AP*UP)-3'(Non-covalent)

A-G-A.1: 9 residues within 4Å: Chain A: T.28, R.29, F.30, K.54, R.56 Chain K: H.32, S.33, E.34, K.35 Protein-ligand interaction information (PLIP) not available A-G-A.2: 9 residues within 4Å: Chain A: H.32, S.33, E.34, K.35 Chain B: T.28, R.29, F.30, K.54, R.56 Protein-ligand interaction information (PLIP) not available A-G-A.3: 9 residues within 4Å: Chain B: H.32, S.33, E.34, K.35 Chain C: T.28, R.29, F.30, K.54, R.56 Protein-ligand interaction information (PLIP) not available A-G-A.4: 11 residues within 4Å: Chain C: G.16, H.32, S.33, E.34, K.35, D.37 Chain D: T.28, R.29, F.30, K.54, R.56 Protein-ligand interaction information (PLIP) not available A-G-A.5: 11 residues within 4Å: Chain D: H.32, S.33, E.34, K.35 Chain E: I.20, T.28, R.29, F.30, S.33, K.54, R.56 Protein-ligand interaction information (PLIP) not available A-G-A.6: 13 residues within 4Å: Chain E: D.15, G.16, H.32, S.33, E.34, K.35, L.36, D.37 Chain F: T.28, R.29, F.30, K.54, R.56 Protein-ligand interaction information (PLIP) not available A-G-A.7: 8 residues within 4Å: Chain F: H.32, S.33, E.34, K.35 Chain G: T.28, F.30, K.54, R.56 Protein-ligand interaction information (PLIP) not available A-G-A.8: 8 residues within 4Å: Chain G: H.32, S.33, E.34, K.35 Chain H: T.28, R.29, F.30, K.54 Protein-ligand interaction information (PLIP) not available A-G-A.9: 9 residues within 4Å: Chain H: H.32, S.33, E.34, K.35 Chain I: T.28, R.29, F.30, K.54, R.56 Protein-ligand interaction information (PLIP) not available A-G-A.10: 9 residues within 4Å: Chain I: H.32, S.33, E.34, K.35 Chain J: T.28, R.29, F.30, K.54, R.56 Protein-ligand interaction information (PLIP) not available A-G-A.11: 9 residues within 4Å: Chain J: H.32, S.33, E.34, K.35 Chain K: T.28, R.29, F.30, K.54, R.56 Protein-ligand interaction information (PLIP) not available

11 x TRP: TRYPTOPHAN(Non-covalent)

TRP.12: 13 residues within 4Å: Chain A: T.23, R.24, G.25, D.27, T.28, S.51 Chain K: G.21, A.44, Q.45, T.47, H.49, T.50, I.53 12 PLIP interactions: 8 interactions with chain K, 4 interactions with chain A, Hydrophobic interactions: K:A.44, K:T.50, K:I.53, A:T.28 Hydrogen bonds: K:Q.45, K:T.47, K:T.50, A:G.25, A:G.25, A:S.51 Water bridges: K:E.48, K:H.49 TRP.13: 13 residues within 4Å: Chain A: G.21, H.32, A.44, Q.45, T.47, H.49, T.50 Chain B: T.23, R.24, G.25, D.27, T.28, S.51 11 PLIP interactions: 4 interactions with chain B, 7 interactions with chain A, Hydrophobic interactions: B:T.28, A:A.44, A:T.50 Hydrogen bonds: B:G.25, B:G.25, B:S.51, A:Q.45, A:T.47, A:T.50 Water bridges: A:E.48 Salt bridges: A:H.31 TRP.14: 14 residues within 4Å: Chain B: G.21, H.32, A.44, Q.45, T.47, H.49, T.50, I.53 Chain C: T.23, R.24, G.25, D.27, T.28, S.51 10 PLIP interactions: 4 interactions with chain C, 6 interactions with chain B, Hydrophobic interactions: C:T.28, B:T.50, B:I.53 Hydrogen bonds: C:G.25, C:G.25, C:S.51, B:Q.45, B:T.47, B:T.50 Water bridges: B:H.49 TRP.15: 15 residues within 4Å: Chain C: G.21, H.31, H.32, A.44, Q.45, T.47, H.49, T.50, I.53 Chain D: T.23, R.24, G.25, D.27, T.28, S.51 12 PLIP interactions: 8 interactions with chain C, 4 interactions with chain D, Hydrophobic interactions: C:A.44, C:T.50, C:I.53, D:T.28 Hydrogen bonds: C:Q.45, C:T.47, C:T.50, D:G.25, D:G.25, D:S.51 Water bridges: C:E.48 Salt bridges: C:H.31 TRP.16: 16 residues within 4Å: Chain D: I.20, G.21, H.31, H.32, A.44, Q.45, T.47, H.49, T.50, I.53 Chain E: T.23, R.24, G.25, D.27, T.28, S.51 13 PLIP interactions: 4 interactions with chain E, 9 interactions with chain D, Hydrophobic interactions: E:T.28, D:A.44, D:T.50, D:I.53 Hydrogen bonds: E:G.25, E:G.25, E:S.51, D:Q.45, D:T.47, D:T.50, D:T.50 Water bridges: D:E.48 Salt bridges: D:H.31 TRP.17: 14 residues within 4Å: Chain E: G.21, H.32, A.44, Q.45, T.47, H.49, T.50, I.53 Chain F: T.23, R.24, G.25, D.27, T.28, S.51 11 PLIP interactions: 4 interactions with chain F, 7 interactions with chain E, Hydrophobic interactions: F:T.28, E:A.44, E:T.50, E:I.53 Hydrogen bonds: F:G.25, F:G.25, F:S.51, E:Q.45, E:T.50 Water bridges: E:E.48 Salt bridges: E:H.31 TRP.18: 14 residues within 4Å: Chain F: G.21, H.32, A.44, Q.45, T.47, H.49, T.50, I.53 Chain G: T.23, R.24, G.25, D.27, T.28, S.51 13 PLIP interactions: 4 interactions with chain G, 9 interactions with chain F, Hydrophobic interactions: G:T.28, F:A.44, F:T.50, F:I.53 Hydrogen bonds: G:G.25, G:G.25, G:S.51, F:Q.45, F:Q.45, F:T.50 Water bridges: F:H.31, F:E.48 Salt bridges: F:H.31 TRP.19: 14 residues within 4Å: Chain G: G.21, H.32, A.44, Q.45, T.47, H.49, T.50, I.53 Chain H: T.23, R.24, G.25, D.27, T.28, S.51 13 PLIP interactions: 10 interactions with chain G, 3 interactions with chain H Hydrophobic interactions: G:A.44, G:T.50, G:I.53 Hydrogen bonds: G:Q.45, G:T.47, G:T.50, H:G.25, H:G.25, H:S.51 Water bridges: G:H.31, G:E.48, G:H.49 Salt bridges: G:H.31 TRP.20: 15 residues within 4Å: Chain H: G.21, H.31, H.32, A.44, Q.45, T.47, H.49, T.50, I.53 Chain I: T.23, R.24, G.25, D.27, T.28, S.51 12 PLIP interactions: 4 interactions with chain I, 8 interactions with chain H, Hydrophobic interactions: I:T.28, H:A.44, H:T.50, H:I.53 Hydrogen bonds: I:G.25, I:G.25, I:S.51, H:Q.45, H:T.47, H:T.50 Water bridges: H:E.48 Salt bridges: H:H.31 TRP.21: 15 residues within 4Å: Chain I: G.21, H.31, H.32, A.44, Q.45, T.47, H.49, T.50, I.53 Chain J: T.23, R.24, G.25, D.27, T.28, S.51 12 PLIP interactions: 8 interactions with chain I, 4 interactions with chain J, Hydrophobic interactions: I:A.44, I:T.50, I:I.53, J:T.28 Hydrogen bonds: I:Q.45, I:T.47, I:T.50, J:G.25, J:G.25, J:S.51 Water bridges: I:E.48 Salt bridges: I:H.31 TRP.22: 14 residues within 4Å: Chain J: G.21, H.32, A.44, Q.45, T.47, H.49, T.50, I.53 Chain K: T.23, R.24, G.25, D.27, T.28, S.51 12 PLIP interactions: 4 interactions with chain K, 8 interactions with chain J, Hydrophobic interactions: K:T.28, J:A.44, J:T.50, J:I.53 Hydrogen bonds: K:G.25, K:G.25, K:S.51, J:Q.45, J:T.47, J:T.50 Water bridges: J:E.48 Salt bridges: J:H.31

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hopcroft, N.H. et al., The Interaction of RNA with Trap: The Role of Triplet Repeats and Separating Spacer Nucleotides. J.Mol.Biol. (2004)

Release Date

2014-07-09

Peptides

TRANSCRIPTION ATTENUATION PROTEIN MTRB: ABCDEFGHIJK

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AA

B
AB

C
AC

D
AD

E
AE

F
AF

G
AG

H
AH

I
AI

J
AJ

K
AK

TRANSCRIPTION ATTENUATION PROTEIN MTRB

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