SMTL ID : 6mv4.1

CRYSTAL STRUCTURE OF HUMAN COAGULATION FACTOR IXa

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.37 Å

Oligo State

hetero-4-4-mer

Ligands

24 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 4 residues within 4Å: Chain A: K.121, R.153, K.220 Ligands: SO4.2 Ligand excluded by PLIP SO4.2: 4 residues within 4Å: Chain A: N.117, K.121 Chain E: A.154 Ligands: SO4.1 Ligand excluded by PLIP SO4.3: 2 residues within 4Å: Chain A: K.113, R.223 Ligand excluded by PLIP SO4.4: 7 residues within 4Å: Chain A: R.158 Chain E: E.114, Y.115, I.118 Chain F: C.3, N.7, C.14 Ligand excluded by PLIP SO4.5: 5 residues within 4Å: Chain A: N.166, R.223 Chain G: N.166, R.223 Ligands: SO4.50 Ligand excluded by PLIP SO4.6: 5 residues within 4Å: Chain A: N.84, F.162, T.163, Y.165 Ligands: FMT.9 Ligand excluded by PLIP SO4.16: 4 residues within 4Å: Chain C: K.121, R.153, K.220 Ligands: SO4.17 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain C: N.117, K.121 Chain G: A.154 Ligands: SO4.16 Ligand excluded by PLIP SO4.18: 2 residues within 4Å: Chain C: K.113, R.223 Ligand excluded by PLIP SO4.19: 7 residues within 4Å: Chain C: R.158 Chain G: E.114, Y.115, I.118 Chain H: C.3, N.7, C.14 Ligand excluded by PLIP SO4.20: 5 residues within 4Å: Chain C: N.166, R.223 Chain E: N.166, R.223 Ligands: SO4.35 Ligand excluded by PLIP SO4.21: 5 residues within 4Å: Chain C: N.84, F.162, T.163, Y.165 Ligands: FMT.24 Ligand excluded by PLIP SO4.31: 4 residues within 4Å: Chain E: K.121, R.153, K.220 Ligands: SO4.32 Ligand excluded by PLIP SO4.32: 4 residues within 4Å: Chain A: A.154 Chain E: N.117, K.121 Ligands: SO4.31 Ligand excluded by PLIP SO4.33: 2 residues within 4Å: Chain E: K.113, R.223 Ligand excluded by PLIP SO4.34: 7 residues within 4Å: Chain A: E.114, Y.115, I.118 Chain B: C.3, N.7, C.14 Chain E: R.158 Ligand excluded by PLIP SO4.35: 5 residues within 4Å: Chain C: N.166, R.223 Chain E: N.166, R.223 Ligands: SO4.20 Ligand excluded by PLIP SO4.36: 5 residues within 4Å: Chain E: N.84, F.162, T.163, Y.165 Ligands: FMT.39 Ligand excluded by PLIP SO4.46: 4 residues within 4Å: Chain G: K.121, R.153, K.220 Ligands: SO4.47 Ligand excluded by PLIP SO4.47: 4 residues within 4Å: Chain C: A.154 Chain G: N.117, K.121 Ligands: SO4.46 Ligand excluded by PLIP SO4.48: 2 residues within 4Å: Chain G: K.113, R.223 Ligand excluded by PLIP SO4.49: 7 residues within 4Å: Chain C: E.114, Y.115, I.118 Chain D: C.3, N.7, C.14 Chain G: R.158 Ligand excluded by PLIP SO4.50: 5 residues within 4Å: Chain A: N.166, R.223 Chain G: N.166, R.223 Ligands: SO4.5 Ligand excluded by PLIP SO4.51: 5 residues within 4Å: Chain G: N.84, F.162, T.163, Y.165 Ligands: FMT.54 Ligand excluded by PLIP

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 5 residues within 4Å: Chain A: G.4, E.5, Y.145, L.146, R.147 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.147 Water bridges: A:R.147, A:R.147 EDO.8: 6 residues within 4Å: Chain A: L.150, D.152 Chain E: G.123, L.150, D.152 Ligands: EDO.38 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:K.121, E:D.152, A:D.152 Water bridges: E:L.150, A:K.121 EDO.22: 5 residues within 4Å: Chain C: G.4, E.5, Y.145, L.146, R.147 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.147 Water bridges: C:R.147, C:R.147 EDO.23: 6 residues within 4Å: Chain C: L.150, D.152 Chain G: G.123, L.150, D.152 Ligands: EDO.53 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain G Hydrogen bonds: C:D.152, G:K.121, G:D.152 Water bridges: C:K.121, G:L.150 EDO.37: 5 residues within 4Å: Chain E: G.4, E.5, Y.145, L.146, R.147 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:R.147 Water bridges: E:R.147, E:R.147 EDO.38: 6 residues within 4Å: Chain A: G.123, L.150, D.152 Chain E: L.150, D.152 Ligands: EDO.8 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:K.121, A:D.152, E:D.152 Water bridges: A:L.150, E:K.121 EDO.52: 5 residues within 4Å: Chain G: G.4, E.5, Y.145, L.146, R.147 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:R.147 Water bridges: G:R.147, G:R.147 EDO.53: 6 residues within 4Å: Chain C: G.123, L.150, D.152 Chain G: L.150, D.152 Ligands: EDO.23 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain G Hydrogen bonds: C:K.121, C:D.152, G:D.152 Water bridges: C:L.150, G:K.121

4 x FMT: FORMIC ACID(Non-functional Binders)

FMT.9: 3 residues within 4Å: Chain A: Y.86, W.205 Ligands: SO4.6 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.84, A:N.84, A:Y.86 FMT.24: 3 residues within 4Å: Chain C: Y.86, W.205 Ligands: SO4.21 3 PLIP interactions: 3 interactions with chain C Water bridges: C:N.84, C:N.84, C:Y.86 FMT.39: 3 residues within 4Å: Chain E: Y.86, W.205 Ligands: SO4.36 3 PLIP interactions: 3 interactions with chain E Water bridges: E:N.84, E:N.84, E:Y.86 FMT.54: 3 residues within 4Å: Chain G: Y.86, W.205 Ligands: SO4.51 3 PLIP interactions: 3 interactions with chain G Water bridges: G:N.84, G:N.84, G:Y.86

4 x PBZ: P-AMINO BENZAMIDINE(Non-covalent)

PBZ.10: 11 residues within 4Å: Chain A: D.179, S.180, C.181, Q.182, S.185, S.204, W.205, G.206, E.207, C.209, G.216 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.179, A:S.180, A:S.185, A:S.185, A:E.207 Water bridges: A:Q.182, A:S.185, A:W.205, A:E.207 PBZ.25: 11 residues within 4Å: Chain C: D.179, S.180, C.181, Q.182, S.185, S.204, W.205, G.206, E.207, C.209, G.216 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:D.179, C:S.180, C:S.185, C:S.185, C:E.207 Water bridges: C:Q.182, C:S.185, C:W.205, C:E.207 PBZ.40: 11 residues within 4Å: Chain E: D.179, S.180, C.181, Q.182, S.185, S.204, W.205, G.206, E.207, C.209, G.216 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:D.179, E:S.180, E:S.185, E:S.185, E:E.207 Water bridges: E:Q.182, E:S.185, E:W.205, E:E.207 PBZ.55: 11 residues within 4Å: Chain G: D.179, S.180, C.181, Q.182, S.185, S.204, W.205, G.206, E.207, C.209, G.216 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:D.179, G:S.180, G:S.185, G:S.185, G:E.207 Water bridges: G:Q.182, G:S.185, G:W.205, G:E.207

4 x CA: CALCIUM ION(Non-covalent)

CA.11: 6 residues within 4Å: Chain A: E.55, N.57, I.58, E.60, E.62, E.65 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:N.57, A:E.60, A:E.62, A:E.65, H2O.1 CA.26: 6 residues within 4Å: Chain C: E.55, N.57, I.58, E.60, E.62, E.65 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:N.57, C:E.60, C:E.62, C:E.65, H2O.18 CA.41: 6 residues within 4Å: Chain E: E.55, N.57, I.58, E.60, E.62, E.65 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:N.57, E:E.60, E:E.62, E:E.65, H2O.35 CA.56: 6 residues within 4Å: Chain G: E.55, N.57, I.58, E.60, E.62, E.65 5 PLIP interactions: 4 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:N.57, G:E.60, G:E.62, G:E.65, H2O.51

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

NA.12: 6 residues within 4Å: Chain A: F.173, H.174, G.176, A.210, M.211, K.214 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.176, A:M.211, A:K.214 Water bridges: A:F.173, A:M.211 NA.27: 6 residues within 4Å: Chain C: F.173, H.174, G.176, A.210, M.211, K.214 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:H.174, C:G.176, C:K.214 Water bridges: C:F.173, C:M.211 NA.42: 6 residues within 4Å: Chain E: F.173, H.174, G.176, A.210, M.211, K.214 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:F.173, E:G.176, E:K.214 Water bridges: E:F.173, E:M.211 NA.57: 6 residues within 4Å: Chain G: F.173, H.174, G.176, A.210, M.211, K.214 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:G.176, G:K.214, G:K.214 Water bridges: G:F.173, G:M.211

12 x CL: CHLORIDE ION(Non-functional Binders)

CL.13: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain A: F.173, R.178 Chain E: R.147 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain A: F.122, E.192 Chain E: H.174 Ligand excluded by PLIP CL.28: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.29: 3 residues within 4Å: Chain C: F.173, R.178 Chain G: R.147 Ligand excluded by PLIP CL.30: 3 residues within 4Å: Chain C: F.122, E.192 Chain G: H.174 Ligand excluded by PLIP CL.43: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.44: 3 residues within 4Å: Chain A: R.147 Chain E: F.173, R.178 Ligand excluded by PLIP CL.45: 3 residues within 4Å: Chain A: H.174 Chain E: F.122, E.192 Ligand excluded by PLIP CL.58: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.59: 3 residues within 4Å: Chain C: R.147 Chain G: F.173, R.178 Ligand excluded by PLIP CL.60: 3 residues within 4Å: Chain C: H.174 Chain G: F.122, E.192 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vadivel, K. et al., Sodium-site in serine protease domain of human coagulation factor IXa: evidence from the crystal structure and molecular dynamics simulations study. J. Thromb. Haemost. (2019)

Release Date

2019-02-20

Peptides

Coagulation factor IX: ACEG
Coagulation factor IX: BDFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

C
H

E
H

G
H

B
L

D
L

F
L

H
L

Coagulation factor IX

Coagulation factor IX

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