6yhj.1 | SWISS-MODEL Template Library

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SMTL ID : 6yhj.1

Thrombin in complex with D-Phe-Pro-2-chlorothiophen derivative (16e)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.44 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

EDO.1:

6 residues within 4Å:

Chain A: E.6, A.7, C.9
Chain B: N.216, R.218, Y.220

2 PLIP interactions:

1 interactions with chain A, 1 interactions with chain B

Hydrogen bonds: A:E.6
Water bridges: B:N.216

2 x NA: SODIUM ION(Non-functional Binders)

NA.2:	5 residues within 4Å: Chain B: D.232, R.233, D.234, G.235, K.236 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.236, B:K.236 Water bridges: B:G.235, B:G.238
NA.3:	4 residues within 4Å: Chain B: K.174, D.175, T.177, R.178 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.174

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4:

7 residues within 4Å:

Chain B: R.89, N.91, N.95, D.97, R.98, R.180, T.182

13 PLIP interactions:

13 interactions with chain B

Hydrogen bonds: B:N.91, B:D.97, B:D.97, B:D.97
Water bridges: B:R.89, B:R.89, B:R.89, B:R.89, B:R.180, B:R.180, B:R.180
Salt bridges: B:R.98, B:R.180

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

NAG.5:

3 residues within 4Å:

Chain B: L.46, P.48, N.53

1 PLIP interactions:

1 interactions with chain B

Hydrophobic interactions: B:L.46

2 x OQZ: (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[(5-chloranylthiophen-2-yl)methyl]pyrrolidine-2-carboxamide(Non-covalent)

OQZ.6:	13 residues within 4Å: Chain A: S.4, G.5, E.6 Chain B: I.33, S.34, L.120, P.121, V.243, F.244, K.247, I.250, Q.251, I.254 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.33, B:L.120, B:K.247, B:K.247, B:I.254, A:E.6, A:E.6
OQZ.7:	20 residues within 4Å: Chain B: H.43, Y.47, W.50, E.94, N.95, L.96, I.179, D.199, A.200, C.201, E.202, S.205, V.225, S.226, W.227, G.228, E.229, G.230, G.238, F.239 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Y.47, B:W.50, B:L.96, B:I.179, B:W.227 Hydrogen bonds: B:S.205, B:S.226, B:G.228 Water bridges: B:G.228, B:G.228, B:G.230 Halogen bonds: B:D.199

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

DMS.8:

4 residues within 4Å:

Chain B: E.124, T.125, S.128, F.215

1 PLIP interactions:

1 interactions with chain B

pi-Cation interactions: B:F.215

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Sandner, A. et al., Thrombin in complex with D-Phe-Pro-2-chlorothiophen derivative (16e). To be published

Release Date

2021-04-14

Peptides

Prothrombin: A
Prothrombin: B
Hirudin variant-2: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

C
I

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Prothrombin

Prothrombin

Hirudin variant-2

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