SMTL ID : 9p0x.1

Nanodisc-embedded human TF/FVIIa/XK1 in complex with 10H10 Fab (nanodisc-subtracted)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-mer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: E.7, E.25, E.29 Ligands: CA.2 No protein-ligand interaction detected (PLIP) MG.4: 6 residues within 4Å: Chain A: E.6, E.7, E.16, E.26 Ligands: CA.2, CA.3 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain A: E.14, E.19 No protein-ligand interaction detected (PLIP) MG.17: 2 residues within 4Å: Chain B: E.14, E.19 No protein-ligand interaction detected (PLIP)

12 x CA: CALCIUM ION(Non-covalent)

CA.2: 7 residues within 4Å: Chain A: E.7, E.25, E.26, E.29 Ligands: MG.1, CA.3, MG.4 No protein-ligand interaction detected (PLIP) CA.3: 6 residues within 4Å: Chain A: E.7, E.16, E.26, E.29 Ligands: CA.2, MG.4 No protein-ligand interaction detected (PLIP) CA.5: 4 residues within 4Å: Chain A: E.6, E.16, E.20, E.26 No protein-ligand interaction detected (PLIP) CA.6: 2 residues within 4Å: Chain A: N.2, E.20 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: 5 interactions with chain A Metal complexes: A:D.46, A:G.47, A:D.63, A:D.63, A:Q.64 CA.11: 3 residues within 4Å: Chain B: E.7, E.25, E.29 No protein-ligand interaction detected (PLIP) CA.12: 7 residues within 4Å: Chain B: N.2, E.7, E.25, E.26, E.29 Ligands: CA.13, CA.14 No protein-ligand interaction detected (PLIP) CA.13: 6 residues within 4Å: Chain B: E.6, E.7, E.16, E.26, E.29 Ligands: CA.12 No protein-ligand interaction detected (PLIP) CA.14: 7 residues within 4Å: Chain B: A.1, N.2, E.6, E.7, E.16, E.26 Ligands: CA.12 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:A.1 CA.15: 5 residues within 4Å: Chain B: A.1, S.3, E.6, E.16, E.20 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:A.1 CA.16: 1 residues within 4Å: Chain B: E.20 No protein-ligand interaction detected (PLIP) CA.18: 5 residues within 4Å: Chain C: E.58, D.60, E.63, H.64, E.68 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.58, C:E.58, C:D.60, C:E.63

1 x BGC: beta-D-glucopyranose(Post Translational Modification)

BGC.8: 3 residues within 4Å: Chain A: S.52, P.54, Y.68 No protein-ligand interaction detected (PLIP)

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

FUC.9: 2 residues within 4Å: Chain A: S.60, F.71 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sedzro, J.C. et al., Cryo-EM structure of the tissue factor/factor VIIa complex with a factor X mimetic reveals a novel allosteric mechanism. Blood (2025)

Release Date

2025-08-27

Peptides

Factor VII light chain: A
Factor X light chain: B
Coagulation factor VII Heavy Chain: C
Tissue factor,Maltose/maltodextrin-binding periplasmic protein: D
Tissue factor pathway inhibitor: E
Human 10H10 antibody Fab heavy chain: F
Human 10H10 antibody Fab light chain: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
V

B
X

C
S

D
T

E
K

F
H

G
L

Factor VII light chain

Factor X light chain

Coagulation factor VII Heavy Chain

Tissue factor,Maltose/maltodextrin-binding periplasmic protein

Tissue factor pathway inhibitor

Human 10H10 antibody Fab heavy chain

Human 10H10 antibody Fab light chain

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