SMTL ID : 2gd4.1 (1 other biounit)

Crystal Structure of the Antithrombin-S195A Factor Xa-Pentasaccharide Complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN.1: 7 residues within 4Å: Chain C: M.28, N.29, P.30, M.31, N.166, T.168, V.366 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.29

1 x ZDO- IDS- SUS- BDP- SGN: 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-deoxy-3,6-di-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-methyl 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranoside

ZDO-IDS-SUS-BDP-SGN.2: 14 residues within 4Å: Chain C: K.22, P.23, R.24, T.55, N.56, R.57, R.58, V.59, S.123, E.124, K.125, F.133, K.136, R.140 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:N.56, C:T.55, C:N.56, C:N.56, C:K.125, C:R.57, C:R.58, C:S.123, C:E.124, C:K.125 Water bridges: C:K.136, C:E.124 Salt bridges: C:K.136, C:R.58, C:K.125, C:R.140, C:K.125, C:K.125, C:K.136, C:R.24, C:R.58, C:K.125

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 6 residues within 4Å: Chain B: D.56, N.58, Q.61, E.62, E.63, E.66 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.56, B:N.58, B:Q.61, B:E.66, H2O.1

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

NAG.4: 1 residues within 4Å: Chain C: N.107 No protein-ligand interaction detected (PLIP) NAG.5: 1 residues within 4Å: Chain C: N.203 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johnson, D.J. et al., Antithrombin-S195A factor Xa-heparin structure reveals the allosteric mechanism of antithrombin activation. Embo J. (2006)

Release Date

2006-05-09

Peptides

Coagulation factor X, Stuart factor, Stuart-Prower factor, Contains: Factor X light chain; Factor X heavy chain; Activated factor Xa heavy chain: A
Coagulation factor, Stuart factor, Stuart-Prower factor, Contains: Factor X light chain; Factor X heavy chain; Activated factor Xa heavy chain: B
Antithrombin-III: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

C
I

Coagulation factor X, Stuart factor, Stuart-Prower factor, Contains: Factor X light chain; Factor X heavy chain; Activated factor Xa heavy chain

Coagulation factor, Stuart factor, Stuart-Prower factor, Contains: Factor X light chain; Factor X heavy chain; Activated factor Xa heavy chain

Antithrombin-III

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