SMTL ID : 1utd.2 (1 other biounit)

The structure of the trp RNA-binding attenuation protein (TRAP) bound to a 63-nucleotide RNA molecule containing GAGUUU repeats

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-11-mer

Ligands

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

G-U-U-U-G-A.1: 16 residues within 4Å: Chain A: G.16, L.22, T.28, R.29, F.30, S.33, E.34, K.35, D.37, K.54, R.56 Chain B: K.54 Chain K: H.32, E.34 Ligands: G-U-A.2, G-U-G-A.11 Protein-ligand interaction information (PLIP) not available G-U-U-U-G-A.2: 14 residues within 4Å: Chain A: H.32, E.34 Chain B: T.28, R.29, F.30, H.32, S.33, E.34, K.35, K.54, R.56 Chain C: K.54 Ligands: G-U-U-U-G-A.1, G-U-G-A.3 Protein-ligand interaction information (PLIP) not available G-U-U-U-G-A.3: 15 residues within 4Å: Chain B: H.32, E.34 Chain C: G.16, T.28, R.29, F.30, S.33, E.34, K.35, D.37, K.54, R.56 Chain D: K.54 Ligands: G-U-A.2, G-U-G-A.4 Protein-ligand interaction information (PLIP) not available G-U-U-U-G-A.4: 16 residues within 4Å: Chain C: H.32, E.34 Chain D: G.16, T.28, R.29, F.30, H.32, S.33, E.34, K.35, D.37, K.54, R.56 Chain E: K.54 Ligands: G-U-G-A.3, G-U-G-A.5 Protein-ligand interaction information (PLIP) not available G-U-U-U-G-A.5: 15 residues within 4Å: Chain D: H.32, E.34 Chain E: G.16, T.28, R.29, F.30, S.33, E.34, K.35, D.37, K.54, R.56 Chain F: K.54 Ligands: G-U-G-A.4, G-U-G-A.6 Protein-ligand interaction information (PLIP) not available G-U-U-U-G-A.6: 15 residues within 4Å: Chain E: H.32, E.34 Chain F: G.16, T.28, R.29, F.30, S.33, E.34, K.35, D.37, K.54, R.56 Chain G: K.54 Ligands: G-U-G-A.5, G-U-G-A.7 Protein-ligand interaction information (PLIP) not available G-U-U-U-G-A.7: 15 residues within 4Å: Chain F: H.32, E.34 Chain G: G.16, T.28, R.29, F.30, S.33, E.34, K.35, D.37, K.54, R.56 Chain H: K.54 Ligands: G-U-G-A.6, G-U-G-A.8 Protein-ligand interaction information (PLIP) not available G-U-U-U-G-A.8: 15 residues within 4Å: Chain G: H.32, E.34 Chain H: G.16, T.28, R.29, F.30, S.33, E.34, K.35, D.37, K.54, R.56 Chain I: K.54 Ligands: G-U-G-A.7, G-U-G-A.9 Protein-ligand interaction information (PLIP) not available G-U-U-U-G-A.9: 14 residues within 4Å: Chain H: H.32, E.34 Chain I: G.16, T.28, R.29, F.30, S.33, E.34, K.35, D.37, K.54, R.56 Ligands: G-U-G-A.8, G-U-G-A.10 Protein-ligand interaction information (PLIP) not available G-U-U-U-G-A.10: 15 residues within 4Å: Chain I: H.32, E.34 Chain J: G.16, T.28, R.29, F.30, S.33, E.34, K.35, D.37, K.54, R.56 Chain K: K.54 Ligands: G-U-G-A.9, G-U-G-A.11 Protein-ligand interaction information (PLIP) not available G-U-U-U-G-A.11: 15 residues within 4Å: Chain A: K.54 Chain J: H.32, E.34 Chain K: G.16, T.28, R.29, F.30, S.33, E.34, K.35, D.37, K.54, R.56 Ligands: G-U-U-U-G-A.1, G-U-G-A.10 Protein-ligand interaction information (PLIP) not available

11 x TRP: TRYPTOPHAN(Non-covalent)

TRP.12: 16 residues within 4Å: Chain A: G.21, H.31, 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 11 PLIP interactions: 4 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:T.28, A:A.44, A:I.53 Hydrogen bonds: B:G.25, B:G.25, B:S.51, A:Q.45, A:Q.45, A:T.50 Water bridges: A:E.48 Salt bridges: A:H.31 TRP.13: 15 residues within 4Å: Chain B: G.21, H.31, 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 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:A.44, B:T.50, B:I.53, C:T.28 Hydrogen bonds: B:Q.45, B:T.47, B:T.50, C:G.25, C:G.25, C:S.51 Water bridges: B:H.31, B:E.48 Salt bridges: B:H.31 TRP.14: 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 13 PLIP interactions: 9 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.47, C:T.50, D:G.25, D:G.25, D:S.51 Water bridges: C:E.48 Salt bridges: C:H.31 TRP.15: 16 residues within 4Å: Chain D: 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, A.52 13 PLIP interactions: 9 interactions with chain D, 4 interactions with chain E Hydrophobic interactions: D:A.44, D:T.50, D:I.53, E:T.28 Hydrogen bonds: D:Q.45, D:Q.45, D:T.47, D:T.50, E:G.25, E:G.25, E:S.51 Water bridges: D:E.48 Salt bridges: D:H.31 TRP.16: 15 residues within 4Å: Chain E: G.21, H.31, 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, A.52 11 PLIP interactions: 7 interactions with chain E, 4 interactions with chain F, Hydrophobic interactions: E:A.44, E:I.53, F:T.28 Hydrogen bonds: E:Q.45, E:T.47, E:T.50, F:G.25, F:G.25, F:S.51 Water bridges: E:E.48 Salt bridges: E:H.31 TRP.17: 15 residues within 4Å: Chain F: G.21, H.31, 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 12 PLIP interactions: 4 interactions with chain G, 8 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:T.47, F:T.50 Water bridges: F:E.48 Salt bridges: F:H.31 TRP.18: 15 residues within 4Å: Chain G: G.21, H.31, 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 11 PLIP interactions: 8 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:E.48 Salt bridges: G:H.31 TRP.19: 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 13 PLIP interactions: 9 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:Q.45, H:T.47, H:T.50, I:G.25, I:G.25, I:S.51 Water bridges: H:E.48 Salt bridges: H:H.31 TRP.20: 15 residues within 4Å: Chain I: G.21, H.31, 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, A.52 12 PLIP interactions: 4 interactions with chain J, 8 interactions with chain I, Hydrophobic interactions: J:T.28, I:A.44, I:I.53 Hydrogen bonds: J:G.25, J:G.25, J:S.51, I:Q.45, I:T.47, I:T.50 Water bridges: I:E.48, I:H.49 Salt bridges: I:H.31 TRP.21: 14 residues within 4Å: Chain J: G.21, H.31, 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 13 PLIP interactions: 9 interactions with chain J, 4 interactions with chain K Hydrophobic interactions: J:A.44, J:T.50, J:I.53, K:T.28 Hydrogen bonds: J:Q.45, J:Q.45, J:T.47, J:T.50, K:G.25, K:G.25, K:S.51 Water bridges: J:H.49 Salt bridges: J:H.31 TRP.22: 15 residues within 4Å: Chain A: T.23, R.24, G.25, D.27, T.28, S.51 Chain K: G.21, H.31, H.32, A.44, Q.45, T.47, H.49, T.50, I.53 11 PLIP interactions: 4 interactions with chain A, 7 interactions with chain K, Hydrophobic interactions: A:T.28, K:A.44, K:T.50, K:I.53 Hydrogen bonds: A:G.25, A:G.25, A:S.51, K:Q.45, K:T.50 Water bridges: K:E.48 Salt bridges: K: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

2004-01-15

Peptides

TRANSCRIPTION ATTENUATION PROTEIN MTRB: ABCDEFGHIJK

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
M

C
N

D
O

E
P

F
Q

G
R

H
S

I
T

J
U

K
V

TRANSCRIPTION ATTENUATION PROTEIN MTRB

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