SMTL ID : 6rfk.1

Crystal structure of EGRCK-inhibited Gla-domainless fIXa (K148Q, R150Q variant)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

hetero-1-1-mer

Ligands

1 x GLU- GLY- AR7- 0QE: GLU-GLY-AR7-0QE(Non-covalent)

GLU-GLY-AR7-0QE.1: 17 residues within 4Å: Chain B: H.41, Y.86, F.162, D.179, S.180, C.181, Q.182, G.183, D.184, S.185, S.204, W.205, G.206, E.207, E.208, C.209, G.216 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:Y.86 Hydrogen bonds: B:Y.86, B:S.180, B:Q.182, B:G.183, B:S.185, B:S.204, B:G.206, B:E.208 Water bridges: B:Y.86, B:Y.86, B:W.205, B:G.206, B:E.208 Salt bridges: B:D.179

1 x B3P: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

B3P.2: 10 residues within 4Å: Chain A: K.8, N.9, R.11, C.12, E.13, K.39, S.40 Chain B: F.122, E.194 Ligands: GOL.5 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:E.194, A:K.8, A:R.11, A:E.13, A:E.13 Water bridges: A:Q.14

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 6 residues within 4Å: Chain B: E.55, N.57, E.60, E.62, E.65 Ligands: GOL.10 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.55, B:N.57, B:E.60, B:E.62, B:E.65

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: C.5, C.16 Chain B: E.114, Y.115, I.118 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.16 Water bridges: A:C.5, A:N.6 GOL.5: 6 residues within 4Å: Chain B: F.122, T.191, E.192, V.193, E.194 Ligands: B3P.2 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.192, B:E.194 Water bridges: B:E.192, B:E.192, B:G.195 GOL.6: 8 residues within 4Å: Chain B: G.20, K.21, V.22, F.25, C.42, V.43, V.47, K.48 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.21, B:V.22, B:K.48 GOL.7: 6 residues within 4Å: Chain B: N.84, Y.86, F.162, T.163, Y.165, W.205 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.84, B:N.84, B:Y.86, B:T.163, B:T.163 Water bridges: B:K.161, B:T.163, B:Y.165 GOL.8: 8 residues within 4Å: Chain B: S.159, T.160, F.162, G.206, E.207, K.214, Y.215, I.217 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.159, B:T.160, B:E.207, B:E.207, B:E.207, B:Y.215, B:Y.215 Water bridges: B:K.161 GOL.9: 5 residues within 4Å: Chain B: D.6, A.140, L.141, V.142, Q.144 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.6, B:L.141, B:V.142 Water bridges: B:D.6 GOL.10: 7 residues within 4Å: Chain B: E.55, N.57, I.58, E.60, T.61, E.65 Ligands: CA.3 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.57, B:T.61 GOL.11: 5 residues within 4Å: Chain B: H.76, N.78, H.88, R.223, Y.224 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.78, B:R.223, B:R.223 GOL.12: 5 residues within 4Å: Chain B: K.113, N.117, K.220, S.222, R.223 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.113, B:N.117, B:K.220, B:K.220, B:S.222, B:R.223 GOL.13: 2 residues within 4Å: Chain B: L.150, D.152 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.152 Water bridges: B:R.153

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sendall, T.J. et al., NMR resonance assignments of apo and EGRCK-inhibited factor IXa. To Be Published

Release Date

2019-06-12

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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