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

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-11-mer

Ligands

11 x TRP: TRYPTOPHAN(Non-covalent)

TRP.1: 12 residues within 4Å: Chain A: T.23, G.25, D.27, T.28, S.51 Chain K: G.21, H.31, A.44, Q.45, T.47, T.50, I.53 9 PLIP interactions: 3 interactions with chain A, 5 interactions with chain K, 1 Ligand-Ligand interactions Hydrophobic interactions: A:T.28, K:A.44, K:T.47, K:I.53, W.1 Hydrogen bonds: A:G.25, A:G.25, K:Q.45, K:Q.45 TRP.2: 16 residues within 4Å: Chain A: I.20, G.21, H.32, A.44, Q.45, T.47, H.49, T.50, I.53 Chain B: T.23, R.24, G.25, D.27, T.28, S.51, A.52 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain A, Hydrophobic interactions: B:T.28, A:T.50, A:I.53 Hydrogen bonds: B:G.25, B:G.25, B:S.51, A:Q.45, A:T.50, A:T.50 Water bridges: A:H.49 TRP.3: 15 residues within 4Å: Chain B: I.20, 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: 7 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:I.53 Hydrogen bonds: B:Q.45, B:Q.45, B:T.50, B:T.50, C:G.25, C:G.25, C:S.51 Water bridges: B:E.48, B:H.49 TRP.4: 14 residues within 4Å: Chain C: G.21, 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 11 PLIP interactions: 7 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:Q.45, C:T.50, C:T.50, D:G.25, D:G.25, D:S.51 TRP.5: 14 residues within 4Å: Chain D: G.21, 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 12 PLIP interactions: 8 interactions with chain D, 4 interactions with chain E, Hydrophobic interactions: D:T.50, D:I.53, E:T.28 Hydrogen bonds: D:Q.45, D:Q.45, D:T.50, D:T.50, E:G.25, E:G.25, E:S.51 Water bridges: D:E.48, D:H.49 TRP.6: 15 residues within 4Å: Chain E: I.20, 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 10 PLIP interactions: 7 interactions with chain E, 3 interactions with chain F, Hydrophobic interactions: E:T.50, E:I.53 Hydrogen bonds: E:Q.45, E:T.50, E:T.50, F:G.25, F:G.25, F:S.51 Water bridges: E:E.48, E:H.49 TRP.7: 15 residues within 4Å: Chain F: I.20, 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 11 PLIP interactions: 4 interactions with chain G, 7 interactions with chain F Hydrophobic interactions: G:T.28, F:T.50, F:I.53 Hydrogen bonds: G:G.25, G:G.25, G:S.51, F:Q.45, F:T.50, F:T.50 Water bridges: F:E.48, F:H.49 TRP.8: 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: 9 interactions with chain G, 4 interactions with chain H, Hydrophobic interactions: G:A.44, G:T.50, G:I.53, H:T.28 Hydrogen bonds: G:Q.45, G:T.47, G:T.50, G:T.50, H:G.25, H:G.25, H:S.51 Water bridges: G:E.48, G:H.49 TRP.9: 14 residues within 4Å: Chain H: G.21, 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, A.52 12 PLIP interactions: 8 interactions with chain H, 4 interactions with chain I, Hydrophobic interactions: H:A.44, H:T.50, H:I.53, I:T.28 Hydrogen bonds: H:Q.45, H:T.47, H:T.50, H:T.50, I:G.25, I:G.25, I:S.51 Water bridges: H:E.48 TRP.10: 15 residues within 4Å: Chain I: I.20, G.21, 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:T.50, I:I.53, J:T.28 Hydrogen bonds: I:Q.45, I:Q.45, I:T.50, I:T.50, J:G.25, J:G.25, J:S.51 Water bridges: I:E.48, I:H.49 TRP.11: 15 residues within 4Å: Chain J: I.20, 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 10 PLIP interactions: 6 interactions with chain J, 4 interactions with chain K, Hydrophobic interactions: J:T.50, J:I.53, K:T.28 Hydrogen bonds: J:Q.45, J:T.50, J:T.50, K:G.25, K:G.25, K:S.51 Water bridges: J:E.48

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
BL

B
BM

C
BN

D
BO

E
BP

F
BQ

G
BR

H
BS

I
BT

J
BU

K
BV

TRANSCRIPTION ATTENUATION PROTEIN MTRB

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