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SMTL ID : 1c1v.1

RECRUITING ZINC TO MEDIATE POTENT, SPECIFIC INHIBITION OF SERINE PROTEASES

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.1:	4 residues within 4Å: Chain B: H.43, S.205, S.226 Ligands: BAB.4 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.43, B:S.205
ZN.2:	3 residues within 4Å: Chain B: E.202, G.230 Ligands: BAB.4 No protein-ligand interaction detected (PLIP)

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

NA.3:

6 residues within 4Å:

Chain B: D.232, R.233, D.234, G.235, K.236, Y.237

4 PLIP interactions:

4 interactions with chain B

Hydrogen bonds: B:K.236, B:K.236
Water bridges: B:R.233, B:G.235

1 x BAB: BIS(5-AMIDINO-BENZIMIDAZOLYL)METHANE(Non-covalent)

BAB.4:

23 residues within 4Å:

Chain B: L.27, C.28, H.43, C.44, W.50, K.52, D.199, A.200, C.201, E.202, S.205, V.225, S.226, W.227, G.228, E.229, G.230, C.231, D.232, G.238, F.239
Ligands: ZN.1, ZN.2

11 PLIP interactions:

11 interactions with chain B

Hydrophobic interactions: B:V.225
Hydrogen bonds: B:L.27, B:K.52, B:D.199, B:D.199, B:A.200, B:E.202, B:E.202
Water bridges: B:E.202, B:Y.240
pi-Stacking: B:W.50

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Katz, B.A. et al., Design of potent selective zinc-mediated serine protease inhibitors. Nature (1998)

Release Date

2000-07-26

Peptides

Thrombin light chain: A
Thrombin heavy chain: B
Hirudin-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-2

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