SMTL ID : 2fir.1

Crystal structure of DFPR-VIIa/sTF

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.1: 4 residues within 4Å: Chain A: Q.49, S.52, P.54, Y.68 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.49, A:S.52 Water bridges: A:Y.68

1 x FUC: alpha-L-fucopyranose(Non-covalent)

FUC.2: 8 residues within 4Å: Chain A: G.58, S.60, F.71, C.72, L.73 Chain C: R.126, R.130, F.135 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:F.135 Hydrogen bonds: C:R.126, A:S.60

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: E.25, R.28, E.29 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain A: E.16, E.26 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain A: E.14, E.19 No protein-ligand interaction detected (PLIP)

6 x CA: CALCIUM ION(Non-covalent)

CA.4: 3 residues within 4Å: Chain A: E.26, E.29 Ligands: CA.5 No protein-ligand interaction detected (PLIP) CA.5: 3 residues within 4Å: Chain A: E.26, E.29 Ligands: CA.4 No protein-ligand interaction detected (PLIP) CA.7: 5 residues within 4Å: Chain A: A.1, E.7, E.16, E.20 Ligands: CA.8 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:A.1, H2O.2 CA.8: 3 residues within 4Å: Chain A: E.6, E.20 Ligands: CA.7 No protein-ligand interaction detected (PLIP) CA.10: 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:D.63, H2O.18 CA.12: 5 residues within 4Å: Chain B: E.58, D.60, E.63, H.64, E.68 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.58, B:D.60, B:E.63, B:E.68, H2O.12, H2O.12

1 x 0G7: D-phenylalanyl-N-[(3S)-6-carbamimidamido-1-chloro-2-oxohexan-3-yl]-L-prolinamide(Covalent)

0G7.11: 20 residues within 4Å: Chain B: H.41, T.86, D.167, S.168, P.169, D.186, S.187, C.188, K.189, G.190, D.191, S.192, S.211, W.212, G.213, Q.214, G.215, C.216, G.223 Ligands: CL.16 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:W.212, B:W.212 Hydrogen bonds: B:S.187, B:S.187, B:G.190, B:D.191, B:S.192, B:S.192, B:S.211, B:G.213, B:G.213, B:G.215 Water bridges: B:Q.214, B:G.215, B:A.217, B:V.224 Salt bridges: B:D.186

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

NA.13: 8 residues within 4Å: Chain B: Y.180, S.181, D.182, G.183, A.217, T.218, V.219, H.221 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.183, B:A.217 Water bridges: B:S.184, B:A.217

2 x ZN: ZINC ION(Non-covalent)

ZN.14: 3 residues within 4Å: Chain B: H.64, E.68, S.70 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.68, H2O.12, H2O.12 ZN.15: 4 residues within 4Å: Chain B: K.9, G.57, D.67, H.105 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:G.57, H2O.8

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

CL.16: 4 residues within 4Å: Chain B: G.213, Q.214, G.215 Ligands: 0G7.11 Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain B: R.71, R.72, H.97, Q.98 Ligand excluded by PLIP CL.18: 7 residues within 4Å: Chain C: D.124, E.125, S.137, L.138, R.139, Y.148, N.168 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bajaj, S.P. et al., High Resolution Structures of p-Aminobenzamidine- and Benzamidine-VIIa/Soluble Tissue Factor: Unpredicted conformation of the 192-193 peptide bond and mapping of Ca2+, Mg2+, Na+ and Zn2+ sites in factor VIIa. J.Biol.Chem. (2006)

Release Date

2006-07-11

Peptides

Coagulation factor VII Light chain: A
Coagulation factor VII Heavy Chain (EC 3.4.21.21): 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 (EC 3.4.21.21)

Tissue factor

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