5qy9.1 | SWISS-MODEL Template Library

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SMTL ID : 5qy9.1

PanDDA analysis group deposition -- Aar2/RNaseH in complex with fragment F2X-Entry C11b

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

hetero-1-1-mer

Ligands

1 x R8Y: N-ethyl-N-(thiophene-2-carbonyl)-beta-alanine(Covalent)

R8Y.1:

8 residues within 4Å:

Chain A: S.5, Y.8, L.129, Y.170, S.174, T.177, L.252, N.255

6 PLIP interactions:

6 interactions with chain A

Hydrophobic interactions: A:L.129, A:L.252, A:N.255
Hydrogen bonds: A:Y.8, A:T.177
pi-Stacking: A:Y.8

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.2:	2 residues within 4Å: Chain A: A.39, T.40 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.40
SO4.3:	3 residues within 4Å: Chain A: K.53, S.168, S.169 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.169 Water bridges: A:S.169, A:Y.170, A:Y.170 Salt bridges: A:K.53
SO4.7:	2 residues within 4Å: Chain A: H.31, K.32 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.32
SO4.8:	4 residues within 4Å: Chain A: T.104, R.105, K.106, K.257 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.106 Water bridges: A:K.257 Salt bridges: A:K.257

3 x PGR: R-1,2-PROPANEDIOL(Non-covalent)

PGR.4:	9 residues within 4Å: Chain A: S.138, I.139, D.140, K.191, L.195, I.202, L.207, W.208, P.209 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.191 Hydrogen bonds: A:D.140 Water bridges: A:K.141, A:L.207
PGR.5:	8 residues within 4Å: Chain A: N.13, N.14, D.15, I.16, K.17, N.51, K.53, T.54 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.17, A:N.51
PGR.6:	4 residues within 4Å: Chain A: E.113, I.122, A.123, I.124 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.113 Hydrogen bonds: A:I.122, A:I.124, A:I.124

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Wollenhaupt, J. et al., F2X-Universal and F2X-Entry: Structurally Diverse Compound Libraries for Crystallographic Fragment Screening. Structure (2020)

Release Date

2020-06-10

Peptides

Pre-mRNA-splicing factor 8: A
A1 cistron-splicing factor AAR2: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Pre-mRNA-splicing factor 8

A1 cistron-splicing factor AAR2

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