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SMTL ID : 5do4.1

Thrombin-RNA aptamer complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 0G6: D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide(Covalent)

0G6.1:

17 residues within 4Å:

Chain B: H.43, Y.47, W.50, E.94, L.96, D.199, A.200, C.201, G.203, D.204, S.205, S.226, W.227, G.228, G.230, C.231, G.238

17 PLIP interactions:

17 interactions with chain B

Hydrophobic interactions: B:Y.47, B:W.50, B:L.96, B:L.96, B:W.227
Hydrogen bonds: B:A.200, B:E.202, B:G.203, B:D.204, B:S.205, B:S.226, B:G.228, B:G.228, B:G.230
Water bridges: B:W.227, B:Y.240
Salt bridges: B:D.199

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2:

2 residues within 4Å:

Chain B: N.53, T.55

1 PLIP interactions:

1 interactions with chain B

Hydrogen bonds: B:N.53

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

EDO.3:	2 residues within 4Å: Chain B: Y.134, F.215 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.134
EDO.4:	3 residues within 4Å: Chain A: L.20 Chain B: K.212, N.217 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.212, A:L.20
EDO.5:	3 residues within 4Å: Chain B: I.9, H.66, E.72 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.70
EDO.6:	6 residues within 4Å: Chain B: A.127, F.244, R.245 Chain C: A.15, G.16, X.18 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.245, B:R.245

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7:	5 residues within 4Å: Chain A: E.6 Chain B: I.33, L.120, Q.251, I.254 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.6, B:Q.251 Water bridges: B:L.120
GOL.8:	2 residues within 4Å: Chain B: E.124, F.215 No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-covalent)

CA.9:

3 residues within 4Å:

Chain B: Y.190, R.233, K.236

6 PLIP interactions:

2 interactions with chain B, 4 Ligand-Water interactions

Metal complexes: B:R.233, B:K.236, H₂O.1, H₂O.3, H₂O.3, H₂O.5

1 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.10:

10 residues within 4Å:

Chain B: L.130, A.132, I.167, V.168, E.169, R.170, F.186, H.242
Chain C: A.14, A.15

5 PLIP interactions:

5 interactions with chain B

Hydrophobic interactions: B:L.130, B:A.132
Hydrogen bonds: B:A.132, B:R.170
Water bridges: B:Q.131

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.11:

3 residues within 4Å:

Chain C: A.7, A.8, A.9

No protein-ligand interaction detected (PLIP)

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Abeydeera, N.D. et al., Evoking picomolar binding in RNA by a single phosphorodithioate linkage. Nucleic Acids Res. (2016)

Release Date

2016-09-14

Peptides

Thrombin light chain: A
Thrombin heavy chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Thrombin light chain

Thrombin heavy chain

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