SMTL ID : 4bxw.1

Crystal Structure of the Prothrombinase Complex from the Venom of Pseudonaja Textilis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.71 Å

Oligo State

hetero-2-1-mer

Ligands

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

0GJ.1: 15 residues within 4Å: Chain A: H.211, Y.262, D.356, A.357, C.358, Q.359, G.360, D.361, S.362, S.381, S.382, G.383, G.385, G.393 Ligands: GOL.3 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:Y.262, A:Y.262, A:A.357, A:Q.359, A:G.360, A:D.361, A:S.362, A:S.381, A:G.383, A:G.385 Water bridges: A:S.382, A:N.394 Salt bridges: A:D.356 0GJ.4: 16 residues within 4Å: Chain B: H.211, Y.262, D.356, A.357, C.358, Q.359, G.360, D.361, S.362, V.380, S.381, S.382, G.383, G.385, C.386, G.393 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:V.380 Hydrogen bonds: B:Y.262, B:Q.359, B:G.360, B:S.362, B:S.381, B:G.383, B:G.385, B:G.385 Water bridges: B:F.195, B:S.382 Salt bridges: B:D.356

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

NA.2: 6 residues within 4Å: Chain A: Y.350, D.351, L.353, A.387, R.388, K.391 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.353

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: H.211, Y.262, Q.359 Ligands: 0GJ.1 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Y.262, A:Y.262 GOL.5: 6 residues within 4Å: Chain B: C.89, R.90, D.92, N.93, Q.294, V.295 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:C.89, B:D.92, B:N.93 GOL.6: 3 residues within 4Å: Chain B: N.293, Q.294, K.298 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.298 Water bridges: B:K.397

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lechtenberg, B.C. et al., Crystal Structure of the Prothrombinase Complex from the Venom of Pseudonaja Textilis. Blood (2013)

Release Date

2013-07-31

Peptides

FACTOR XA: AB
COAGULATION FACTOR V: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
F

FACTOR XA

COAGULATION FACTOR V

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