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SMTL ID : 3e6p.1

Crystal structure of human meizothrombin desF1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-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:

3 residues within 4Å:

Chain A: K.74
Chain B: L.46, N.53

1 PLIP interactions:

1 interactions with chain A

Hydrogen bonds: A:K.74

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.2:

7 residues within 4Å:

Chain A: E.92, E.93, T.94, G.95, D.96
Chain B: R.170, R.245

7 PLIP interactions:

3 interactions with chain A, 4 interactions with chain B

Hydrogen bonds: A:E.93, A:D.96
Water bridges: A:T.94, B:R.170, B:H.242
Salt bridges: B:R.170, B:R.245

1 x DFK: D-PHENYLALANYL-N-[(1S)-4-{[(Z)-AMINO(IMINO)METHYL]AMINO}-1-(CHLOROACETYL)BUTYL]-L-PROLINAMIDE(Covalent)

DFK.3:

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, G.203, D.204, S.205, S.226, W.227, G.228, G.230, C.231, G.238

17 PLIP interactions:

17 interactions with chain B

Hydrophobic interactions: B:Y.47, B:W.50, B:I.179, B:W.227
Hydrogen bonds: B:A.200, B:G.203, B:D.204, B:S.205, B:S.226, B:G.228, B:G.228, B:G.230
Water bridges: B:W.227, B:G.230, B:D.232, B:Y.240
Salt bridges: B:D.199

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

NA.4:

3 residues within 4Å:

Chain B: Y.190, R.233, K.236

4 PLIP interactions:

4 interactions with chain B

Hydrogen bonds: B:R.233, B:K.236
Water bridges: B:R.197, B:G.235

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Papaconstantinou, M.E. et al., Na(+) binding to meizothrombin desF1. Cell.Mol.Life Sci. (2008)

Release Date

2008-11-18

Peptides

Prothrombin: A
Prothrombin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Prothrombin

Prothrombin

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