SMTL ID : 5jbb.1

Crystal structure of factor IXa variant V16I K98T Y177T I213V in complex with EGR-chloromethylketone

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

hetero-1-1-mer

Ligands

1 x CA: CALCIUM ION(Non-covalent)

CA.1: 8 residues within 4Å: Chain B: E.55, H.56, N.57, I.58, E.60, T.61, E.62, E.65 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.55, B:N.57, B:E.62, B:E.65, H2O.3

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

0GJ.2: 22 residues within 4Å: Chain B: F.25, C.26, H.41, C.42, Y.86, H.135, D.179, S.180, C.181, Q.182, G.183, D.184, S.185, V.203, S.204, W.205, G.206, E.207, E.208, C.209, A.210, G.216 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:Y.86, B:S.180, B:S.180, B:Q.182, B:G.183, B:D.184, B:S.185, B:S.204, B:G.206, B:E.208 Water bridges: B:Y.86, B:Q.182, B:W.205, B:E.208, B:A.210 Salt bridges: B:D.179

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 8 residues within 4Å: Chain B: D.6, V.133, R.138, S.139, A.140, L.141, V.142, Q.144 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.141, B:V.142 Salt bridges: B:D.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kristensen, L.H. et al., Releasing the brakes in coagulation Factor IXa by co-operative maturation of the substrate-binding site. Biochem.J. (2016)

Release Date

2016-06-01

Peptides

Coagulation factor IX: A
Coagulation factor IX: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
S

Coagulation factor IX

Coagulation factor IX

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