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SMTL ID : 5mls.1

Thrombin Mutant A190S in complex with (S)-1-(D-phenylalanyl)-N-(3-chlorobenzyl)pyrrolidine-2-carboxamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.62 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x 22U: D-phenylalanyl-N-(3-chlorobenzyl)-L-prolinamide(Non-covalent)

22U.1:

19 residues within 4Å:

Chain B: H.43, Y.47, W.50, E.94, N.95, L.96, I.179, S.200, C.201, S.205, V.225, S.226, W.227, G.228, E.229, G.230, G.238, F.239
Ligands: GOL.9

9 PLIP interactions:

9 interactions with chain B

Hydrophobic interactions: B:Y.47, B:W.50, B:I.179, B:V.225, B:W.227
Hydrogen bonds: B:S.226, B:G.228, B:G.228
Water bridges: B:G.230

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

DMS.2:

7 residues within 4Å:

Chain B: L.130, Q.131, A.132, I.167, V.168, R.170, F.186

1 PLIP interactions:

1 interactions with chain B

Hydrogen bonds: B:R.170

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

PO4.3:

1 residues within 4Å:

Ligands: GOL.6

No protein-ligand interaction detected (PLIP)

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4:	5 residues within 4Å: Chain B: R.170, D.183, H.242, R.245 Ligands: GOL.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.183, B:D.183
GOL.5:	1 residues within 4Å: Chain B: F.215 No protein-ligand interaction detected (PLIP)
GOL.6:	6 residues within 4Å: Chain B: R.170, I.181, T.182, D.183 Ligands: PO4.3, GOL.4 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.170, B:R.170 Water bridges: B:D.183, B:D.183
GOL.7:	3 residues within 4Å: Chain B: R.89, N.91, R.98 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.89, B:R.89, B:N.91, B:R.98, B:R.98
GOL.8:	3 residues within 4Å: Chain B: D.175, S.176, G.235 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.175
GOL.9:	8 residues within 4Å: Chain B: L.27, C.28, W.50, K.52, E.202, G.203, S.205 Ligands: 22U.1 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.27, B:G.203, B:S.205

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

NA.10:	4 residues within 4Å: Chain B: K.174, D.175, T.177, R.178 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.177 Water bridges: B:K.174
NA.11:	5 residues within 4Å: Chain B: D.232, R.233, D.234, G.235, K.236 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.236, B:K.236 Water bridges: B:G.235

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Marca, A. et al., Thrombin Mutante A190S in complex with (S)-1-((R)-2-amino-3,3-diphenylpropanoyl)-N-(4-carbamimidoylbenzyl)pyrrolidine-2-carboxamide. to be published

Release Date

2017-12-20

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
D

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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