SMTL ID : 3kcg.1

Crystal structure of the antithrombin-factor IXa-pentasaccharide complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 1 residues within 4Å: Chain C: N.96 1 PLIP interactions: 1 interactions with chain C Water bridges: C:I.22, C:D.97 NAG-FUC.3: 2 residues within 4Å: Chain C: N.192, K.193 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.193, C:K.193, C:K.193

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

NAG-NAG-MAN.2: 5 residues within 4Å: Chain C: N.18, P.19, M.20, N.155, T.157 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.18

1 x Z9L- Z9K- GU6- GU1- Z9H: 3,4-di-O-methyl-2,6-di-O-sulfo-alpha-D-glucopyranose-(1-4)-2,3-di-O-methyl-beta-D-glucopyranuronic acid-(1-4)-2,3,6-tri-O-sulfo-alpha-D-glucopyranose-(1-4)-3-O-methyl-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-methyl 2,3,6-tri-O-sulfo-alpha-D-glucopyranoside(Post Translational Modification)

Z9L-Z9K-GU6-GU1-Z9H.4: 15 residues within 4Å: Chain C: K.11, P.12, R.13, A.43, T.44, N.45, R.47, V.48, S.112, E.113, K.114, F.121, F.122, K.125, R.129 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:N.45, C:R.13, C:N.45, C:T.44, C:T.44, C:N.45, C:K.114, C:S.112, C:E.113, C:K.114 Water bridges: C:K.125, C:A.43, C:R.129, C:R.129, C:R.47, C:R.47, C:K.114, C:D.117 Salt bridges: C:K.125, C:K.114, C:K.114, C:K.125, C:R.129, C:R.13, C:R.47, C:K.114, C:R.13, C:R.47, C:R.47, C:K.114

1 x CA: CALCIUM ION(Non-covalent)

CA.5: 5 residues within 4Å: Chain B: E.55, N.57, E.60, E.62, E.65 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.55, B:N.57, B:E.60, B:E.62, B:E.65, H2O.3

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.6: 8 residues within 4Å: Chain C: L.81, N.127, L.130, Y.131, L.140, S.142, I.219 Ligands: MPD.7 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.81, C:N.127, C:L.130, C:L.140 Hydrogen bonds: C:S.142 MPD.7: 7 residues within 4Å: Chain C: C.8, A.124, C.128, V.165, Y.166, G.167 Ligands: MPD.6 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:A.124 Water bridges: C:N.144

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johnson, D.J. et al., Molecular basis of factor IXa recognition by heparin-activated antithrombin revealed by a 1.7-A structure of the ternary complex. Proc.Natl.Acad.Sci.USA (2010)

Release Date

2010-02-02

Peptides

Coagulation factor IXa light chain: A
Coagulation factor IXa heavy chain: B
Antithrombin-III: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

C
I

Coagulation factor IXa light chain

Coagulation factor IXa heavy chain

Antithrombin-III

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