SMTL ID : 3dd2.1

Crystal structure of an RNA aptamer bound to human thrombin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-1-1-mer

Ligands

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.1: 7 residues within 4Å: Chain A: Y.28, I.29, D.30 Chain B: Q.131, A.132, Y.134 Chain C: A.14 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:I.29, B:Q.131, B:Y.134 PEG.12: 4 residues within 4Å: Chain C: G.3, A.4, C.23, C.24 No protein-ligand interaction detected (PLIP) PEG.13: 4 residues within 4Å: Chain C: C.11, U.12, C.19, U.20 No protein-ligand interaction detected (PLIP)

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

0G6.2: 19 residues within 4Å: Chain B: H.43, Y.47, W.50, E.94, N.95, L.96, D.199, A.200, C.201, E.202, G.203, D.204, S.205, S.226, W.227, G.228, G.230, C.231, G.238 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:Y.47, B:L.96, B:L.96, B:W.227 Hydrogen bonds: B:A.200, B:G.203, B:S.205, B:S.226, B:G.228, B:G.228, B:G.230 Water bridges: B:W.227, B:G.230, B:G.230, B:Y.240 Salt bridges: B:D.199

2 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.3: 3 residues within 4Å: Chain B: D.232, R.233, K.236 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:R.233, B:K.236, H2O.2, H2O.3, H2O.3 MG.9: 3 residues within 4Å: Chain C: A.7, A.8, A.9 No protein-ligand interaction detected (PLIP)

1 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.4: 5 residues within 4Å: Chain B: Q.24, L.60, R.62, Y.71, I.78 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.24, B:Y.71, B:Y.71

6 x ACY: ACETIC ACID(Non-functional Binders)

ACY.5: 2 residues within 4Å: Chain B: N.53 Ligands: ACY.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.53 ACY.6: 2 residues within 4Å: Chain B: G.4, S.5 No protein-ligand interaction detected (PLIP) ACY.7: 1 residues within 4Å: Chain B: R.178 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.178 ACY.8: 2 residues within 4Å: Chain B: N.53 Ligands: ACY.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.53 ACY.10: 4 residues within 4Å: Chain C: A.4, A.5, A.22, C.23 No protein-ligand interaction detected (PLIP) ACY.11: 3 residues within 4Å: Chain C: G.2, G.3, A.4 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Long, S.B. et al., Crystal structure of an RNA aptamer bound to thrombin. Rna (2008)

Release Date

2008-11-11

Peptides

Thrombin light chain: A
Thrombin heavy chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

Thrombin light chain

Thrombin heavy chain

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