SMTL ID : 2b8o.1

Crystal Structure of Glu-Gly-Arg-Chloromethyl Ketone-Factor VIIa/Soluble Tissue Factor Complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x GLC: alpha-D-glucopyranose(Post Translational Modification)

GLC.1: 4 residues within 4Å: Chain A: Q.49, S.52, P.54, Y.68 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.49, A:Y.68

1 x FUC: alpha-L-fucopyranose(Post Translational Modification)

FUC.2: 5 residues within 4Å: Chain A: G.58, S.60 Chain C: R.126, R.130, F.135 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain C Water bridges: A:S.60 Hydrophobic interactions: C:F.135 Hydrogen bonds: C:R.126, C:R.126

6 x CA: CALCIUM ION(Non-covalent)

CA.3: 3 residues within 4Å: Chain A: E.25, E.26, E.29 No protein-ligand interaction detected (PLIP) CA.4: 2 residues within 4Å: Chain A: E.26, E.29 No protein-ligand interaction detected (PLIP) CA.6: 3 residues within 4Å: Chain A: A.1, E.7, E.16 No protein-ligand interaction detected (PLIP) CA.7: 2 residues within 4Å: Chain A: E.6, E.20 No protein-ligand interaction detected (PLIP) CA.9: 5 residues within 4Å: Chain A: D.46, G.47, Q.49, D.63, Q.64 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.46, A:G.47, A:D.63, A:Q.64, H2O.2 CA.11: 6 residues within 4Å: Chain B: E.58, D.60, L.61, E.63, H.64, E.68 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.58, B:D.60, B:E.63, B:E.68

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain A: A.1, E.16, E.26 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain A: E.14, E.19 No protein-ligand interaction detected (PLIP)

1 x 0GJ: L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide(Non-covalent)

0GJ.10: 15 residues within 4Å: Chain B: H.41, D.137, D.186, S.187, C.188, K.189, G.190, D.191, S.192, S.211, W.212, G.213, Q.214, G.215 Ligands: CL.15 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:H.41, B:S.187, B:S.187, B:C.188, B:G.190, B:D.191, B:S.192, B:S.192, B:G.215, B:G.215 Salt bridges: B:D.186

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

NA.12: 6 residues within 4Å: Chain B: Y.180, S.181, D.186, A.217, T.218, H.221 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.186, B:D.186, B:T.218

2 x ZN: ZINC ION(Non-covalent)

ZN.13: 2 residues within 4Å: Chain B: H.64, S.70 No protein-ligand interaction detected (PLIP) ZN.14: 5 residues within 4Å: Chain B: K.9, G.57, H.59, D.67, H.105 No protein-ligand interaction detected (PLIP)

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.15: 3 residues within 4Å: Chain B: G.213, G.215 Ligands: 0GJ.10 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain B: R.71, R.72, H.97, Q.98 Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain C: D.124, E.125, Y.148, N.168 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bajaj, S.P. et al., Crystal Structure of Factor VIIa/soluble Tissue Factor complexed with Glu-Gly-Arg-Chloromethyl ketone. To be published

Release Date

2007-02-13

Peptides

Coagulation factor VII light chain: A
Coagulation factor VII heavy chain: B
Tissue factor: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

C
T

Coagulation factor VII light chain

Coagulation factor VII heavy chain

Tissue factor

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