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SMTL ID : 7ac9.1

Thrombin in complex with D-arginine (j77)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.39 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NA.1:	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.2:	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

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

DMS.3:	5 residues within 4Å: Chain B: E.94, N.95, L.96, I.179, W.227 No protein-ligand interaction detected (PLIP)
DMS.4:	3 residues within 4Å: Chain B: S.176, G.235, K.236 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.236

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

PO4.5:

7 residues within 4Å:

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

8 PLIP interactions:

8 interactions with chain B

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

1 x DAR: D-ARGININE(Non-covalent)

DAR.6:

14 residues within 4Å:

Chain B: D.199, A.200, C.201, E.202, G.203, D.204, S.205, V.225, S.226, W.227, G.228, G.230, C.231, G.238

12 PLIP interactions:

12 interactions with chain B

Hydrogen bonds: B:A.200, B:C.201, B:G.203, B:D.204, B:S.205, B:G.230
Water bridges: B:S.205, B:W.227, B:G.228, B:G.230, B:Y.240
Salt bridges: B:D.199

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

NAG.7:

4 residues within 4Å:

Chain B: L.46, P.48, N.53, W.92

2 PLIP interactions:

2 interactions with chain B

Hydrophobic interactions: B:L.46
Hydrogen bonds: B:N.53

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Scanlan, W. et al., Thrombin in complex with D-arginine (j77). To be published

Release Date

2021-10-06

Peptides

Thrombin light chain: A
Thrombin heavy chain: 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

Thrombin light chain

Thrombin heavy chain

Hirudin variant-2

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