SMTL ID : 2h9e.1

Crystal Structure of FXa/selectide/NAPC2 ternary complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x DTY- ILE- ARG- LEU- LPD: selectide inhibitor DTY-ILE-ARG-LEU-LPD peptide(Non-covalent)

DTY-ILE-ARG-LEU-LPD.1: 21 residues within 4Å: Chain A: H.42, E.83, T.84, Y.85, E.135, S.161, F.162, D.179, A.180, C.181, Q.182, S.185, V.203, S.204, W.205, G.206, E.207, G.208, C.209, R.211, G.216 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:E.135, A:V.203 Hydrogen bonds: A:E.83, A:S.185, A:S.204, A:W.205, A:G.206, A:G.206 Water bridges: A:W.205 pi-Cation interactions: A:F.162, A:W.205, A:W.205

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 4 residues within 4Å: Chain A: Y.173, D.174, T.175, K.176 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.174, A:T.175, A:T.175, A:K.176 PO4.3: 3 residues within 4Å: Chain A: R.101, M.102 Chain B: Y.85 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:M.102, B:Y.85, B:Y.85, B:Y.85 Salt bridges: A:R.101 PO4.4: 3 residues within 4Å: Chain A: G.64, G.65, R.101 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.65 Salt bridges: A:R.101 PO4.5: 2 residues within 4Å: Chain A: Q.5, E.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.6, A:E.6 PO4.6: 2 residues within 4Å: Chain A: R.112, K.226 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.112 Salt bridges: A:R.112, A:K.226 PO4.7: 3 residues within 4Å: Chain A: Q.177, R.211, K.212 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.177, A:K.212

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.8: 2 residues within 4Å: Chain A: T.133, K.144 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.144, A:K.144 Salt bridges: A:K.144 ACT.9: 3 residues within 4Å: Chain A: R.192, K.194, D.195 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.194, A:D.195 Water bridges: A:R.192, A:R.192 Salt bridges: A:R.192 ACT.10: 4 residues within 4Å: Chain A: R.153, K.157, I.164, Q.166 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.164, A:Q.166 Salt bridges: A:R.153, A:K.157

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

NA.11: 5 residues within 4Å: Chain A: Y.173, K.176, A.210, R.211, K.214 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.173 Water bridges: A:Y.173

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Murakami, M.T. et al., Intermolecular Interactions and Characterization of the Novel Factor Xa Exosite Involved in Macromolecular Recognition and Inhibition: Crystal Structure of Human Gla-domainless Factor Xa Complexed with the Anticoagulant Protein NAPc2 from the Hematophagous Nematode Ancylostoma caninum. J.Mol.Biol. (2007)

Release Date

2007-02-13

Peptides

Coagulation factor X heavy chain: A
Coagulation factor X light chain: B
Anti-coagulant protein C2: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
C

Coagulation factor X heavy chain

Coagulation factor X light chain

Anti-coagulant protein C2

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