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SMTL ID : 5rce.1

PanDDA analysis group deposition -- Endothiapepsin changed state model for fragment F2X-Entry Library H05a

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.05 Å

Oligo State

monomer

Ligands

3 x RE4: 6-methyl-N~4~-[(pyridin-3-yl)methyl]pyrimidine-2,4-diamine(Non-covalent)

RE4.1:	11 residues within 4Å: Chain A: D.122, D.124, Y.168, D.170, S.172, S.204, F.205, L.214, G.310 Ligands: RE4.2, DMS.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.205, A:L.214 Hydrogen bonds: A:S.172, A:S.172, A:G.310 Salt bridges: A:D.170
RE4.2:	10 residues within 4Å: Chain A: I.99, D.104, A.105, D.122, D.208, I.211, T.312 Ligands: RE4.1, DMS.4, PG4.8 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.105, A:I.211 Hydrogen bonds: A:T.312, A:T.312 Salt bridges: A:D.104, A:D.208
RE4.3:	6 residues within 4Å: Chain A: C.344, D.368, G.370, P.371, C.379 Ligands: ACT.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.344 Salt bridges: A:D.368

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.4:

6 residues within 4Å:

Chain A: D.170, G.310, T.311, T.312
Ligands: RE4.1, RE4.2

4 PLIP interactions:

4 interactions with chain A

Hydrogen bonds: A:T.312
Water bridges: A:T.312, A:L.313
Salt bridges: A:D.170

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5:	5 residues within 4Å: Chain A: V.361, Y.366, A.401, S.418, K.419 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.366, A:S.418, A:K.419 Water bridges: A:V.361, A:V.361
GOL.6:	6 residues within 4Å: Chain A: P.317, S.386, A.387, G.390, I.391, N.392 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.390, A:G.390 Water bridges: A:A.318, A:G.388, A:N.392

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.7:

5 residues within 4Å:

Chain A: C.344, D.368, G.370, C.379
Ligands: RE4.3

1 PLIP interactions:

1 interactions with chain A

Hydrogen bonds: A:D.368

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.8:

9 residues within 4Å:

Chain A: D.104, T.312, L.313, Y.315, V.337, F.369, I.372, F.380
Ligands: RE4.2

2 PLIP interactions:

2 interactions with chain A

Hydrogen bonds: A:Y.315, A:V.337

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

2020-06-03

Peptides

Endothiapepsin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Endothiapepsin

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