SMTL ID : 6r2w.1

Crystal structure of the super-active FVIIa variant VYT in complex with tissue factor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x BGC- XYS- XYS: alpha-D-xylopyranose-(1-3)-alpha-D-xylopyranose-(1-3)-beta-D-glucopyranose

BGC-XYS-XYS.1: 9 residues within 4Å: Chain A: Q.49, S.52, P.54, Q.66, S.67, Y.68, R.79, N.80 Chain C: I.22 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.52, A:Y.68, A:Y.68, A:R.79 Water bridges: A:A.51, A:Y.68

9 x CA: CALCIUM ION(Non-covalent)

CA.2: 8 residues within 4Å: Chain A: D.46, G.47, D.48, Q.49, D.63, Q.64, L.65, Q.66 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.5 CA.3: 6 residues within 4Å: Chain A: N.2, E.7, E.25, E.26, E.29 Ligands: CA.4 No protein-ligand interaction detected (PLIP) CA.4: 7 residues within 4Å: Chain A: E.7, G.11, E.16, E.26, E.29 Ligands: CA.3, CA.5 No protein-ligand interaction detected (PLIP) CA.5: 8 residues within 4Å: Chain A: A.1, N.2, E.6, E.7, E.16, E.26 Ligands: CA.4, CA.6 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:A.1 CA.6: 7 residues within 4Å: Chain A: A.1, N.2, E.6, R.15, E.16, E.20 Ligands: CA.5 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:A.1, H2O.5 CA.7: 2 residues within 4Å: Chain A: E.14, E.19 No protein-ligand interaction detected (PLIP) CA.8: 1 residues within 4Å: Chain A: E.20 No protein-ligand interaction detected (PLIP) CA.9: 3 residues within 4Å: Chain A: E.25, R.28, E.29 No protein-ligand interaction detected (PLIP) CA.12: 8 residues within 4Å: Chain B: E.58, H.59, D.60, L.61, E.63, H.64, D.65, E.68 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.58, B:D.60, B:E.68, H2O.10, H2O.15

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

FUC.10: 8 residues within 4Å: Chain A: G.58, G.59, S.60, F.71, C.72, L.73 Chain C: R.131, F.140 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:F.140 Hydrogen bonds: C:R.131, C:R.131, A:G.58

10 x TMA: TETRAMETHYLAMMONIUM ION(Non-covalent)(Non-functional Binders)

TMA.11: 7 residues within 4Å: Chain A: K.62, D.63, Q.64 Chain C: Q.110, P.111, T.112, P.206 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.63 TMA.14: 5 residues within 4Å: Chain B: V.55, H.64, E.68, Q.69, S.70 1 PLIP interactions: 1 interactions with chain B pi-Cation interactions: B:H.64 TMA.15: 4 residues within 4Å: Chain B: L.61, S.62, E.63, H.64 1 PLIP interactions: 1 interactions with chain B pi-Cation interactions: B:H.64 TMA.16: 3 residues within 4Å: Chain B: D.177, V.214, G.215 No protein-ligand interaction detected (PLIP) TMA.17: 4 residues within 4Å: Chain B: F.126, N.149, Y.175, K.180 1 PLIP interactions: 1 interactions with chain B pi-Cation interactions: B:F.126 TMA.18: 4 residues within 4Å: Chain B: I.53, S.70, R.71, R.72 No protein-ligand interaction detected (PLIP) TMA.19: 4 residues within 4Å: Chain C: T.172, E.174, F.175, L.176 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:E.174 TMA.20: 10 residues within 4Å: Chain A: V.92 Chain B: R.119, F.123 Chain C: T.35, Q.37, S.47, Y.51, F.76, Y.78, P.92 1 PLIP interactions: 1 interactions with chain C pi-Cation interactions: C:F.76 TMA.21: 7 residues within 4Å: Chain C: K.68, Y.103, V.146, F.147, G.148, K.149, D.150 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:D.150 TMA.22: 3 residues within 4Å: Chain C: Q.114, S.115, T.126 No protein-ligand interaction detected (PLIP)

1 x 0Z7: N-acetyl-D-phenylalanyl-N-[(2S,3S)-6-carbamimidamido-1-chloro-2-hydroxyhexan-3-yl]-L-phenylalaninamide(Covalent)

0Z7.13: 25 residues within 4Å: Chain B: C.26, H.41, C.42, G.85, T.86, T.87, K.165, D.181, S.182, C.183, K.184, G.185, D.186, S.187, V.205, S.206, W.207, G.208, Q.209, G.210, C.211, A.212, G.218, V.219, Y.220 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:V.205, B:W.207 Hydrogen bonds: B:S.182, B:S.182, B:K.184, B:G.185, B:S.187, B:S.206, B:G.208, B:G.208, B:G.210, B:G.210, B:G.210 Water bridges: B:W.207 Salt bridges: B:D.181

Links

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Citation

Sorensen, A.B. et al., Beating tissue factor at its own game: Design and properties of a soluble tissue factor-independent coagulation factor VIIa. J.Biol.Chem. (2020)

Release Date

2019-12-11

Peptides

Coagulation factor VII: A
Coagulation factor VII: B
Tissue factor: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

C
T

Coagulation factor VII

Coagulation factor VII

Tissue factor

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