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SMTL ID : 1k21.1

HUMAN THROMBIN-INHIBITOR COMPLEX

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1:

2 residues within 4Å:

Chain B: N.53, T.55

No protein-ligand interaction detected (PLIP)

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

NA.2:	3 residues within 4Å: Chain B: D.232, R.233, K.236 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.236, B:K.236 Water bridges: B:R.197
NA.3:	3 residues within 4Å: Chain B: K.174, D.175, T.177 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.174

1 x IGN: {[(1R)-2-((2S)-2-{[(3-{[AMINO(IMINO)METHYL]AMINO}PROPYL)AMINO]CARBONYL}PIPERIDINYL)-1-(CYCLOHEXYLMETHYL)-2-OXOETHYL]AMINO}ACETIC ACID(Non-covalent)

IGN.4:

17 residues within 4Å:

Chain B: H.43, Y.47, W.50, E.94, N.95, L.96, D.199, A.200, C.201, S.205, V.225, S.226, W.227, G.228, E.229, G.230, G.238

15 PLIP interactions:

15 interactions with chain B

Hydrophobic interactions: B:Y.47, B:W.50, B:L.96, B:V.225, B:W.227
Hydrogen bonds: B:A.200, B:S.226, B:G.228, B:G.228, B:G.230, B:G.230
Water bridges: B:E.202, B:W.227, B:Y.240
Salt bridges: B:D.199

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Dullweber, F. et al., Factorising ligand affinity: a combined thermodynamic and crystallographic study of trypsin and thrombin inhibition. J.Mol.Biol. (2001)

Release Date

2002-05-08

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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