SMTL ID : 3bg8.2 (1 other biounit)

Crystal structure of Factor XIa in complex with Clavatadine A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-trimer

Ligands

3 x G0R: N-(4-carbamimidamidobutyl)ethanamide(Covalent)

G0R.1: 16 residues within 4Å: Chain A: H.44, D.182, A.183, C.184, K.185, G.186, D.187, S.188, S.207, W.208, G.209, G.211, C.212, G.219 Ligands: BEN.2, SO4.3 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:A.183, A:G.186, A:D.187, A:S.188, A:S.207 Water bridges: A:D.182, A:D.182, A:G.209, A:G.209, A:E.210, A:E.210, A:V.220 Salt bridges: A:D.182 G0R.8: 16 residues within 4Å: Chain B: H.44, D.182, A.183, C.184, K.185, G.186, D.187, S.188, S.207, W.208, G.209, G.211, C.212, G.219 Ligands: BEN.9, SO4.10 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:A.183, B:G.186, B:D.187, B:S.188, B:S.207 Water bridges: B:D.182, B:G.209, B:G.209, B:E.210, B:E.210, B:G.211, B:V.220 Salt bridges: B:D.182 G0R.15: 16 residues within 4Å: Chain C: H.44, D.182, A.183, C.184, K.185, G.186, D.187, S.188, S.207, W.208, G.209, G.211, C.212, G.219 Ligands: BEN.16, SO4.17 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:A.183, C:G.186, C:D.187, C:S.188, C:S.207, C:G.211 Water bridges: C:D.182, C:G.209, C:G.209, C:E.210, C:V.220, C:Y.221 Salt bridges: C:D.182

3 x BEN: BENZAMIDINE(Non-functional Binders)

BEN.2: 13 residues within 4Å: Chain A: D.182, A.183, C.184, K.185, S.188, T.206, S.207, W.208, G.211, C.212, G.219 Ligands: G0R.1, SO4.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.206 Hydrogen bonds: A:W.208 Water bridges: A:W.208, A:G.209, A:E.210 BEN.9: 13 residues within 4Å: Chain B: D.182, A.183, C.184, K.185, S.188, T.206, S.207, W.208, G.211, C.212, G.219 Ligands: G0R.8, SO4.10 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:T.206 Hydrogen bonds: B:W.208 Water bridges: B:W.208, B:G.209, B:E.210 BEN.16: 13 residues within 4Å: Chain C: D.182, A.183, C.184, K.185, S.188, T.206, S.207, W.208, G.211, C.212, G.219 Ligands: G0R.15, SO4.17 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:T.206 Hydrogen bonds: C:D.182, C:G.211 Water bridges: C:W.208, C:G.209, C:E.210

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

SO4.3: 6 residues within 4Å: Chain A: H.44, K.185, G.186, S.188 Ligands: G0R.1, BEN.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.186, A:S.188 Water bridges: A:L.28 Salt bridges: A:H.44 SO4.4: 2 residues within 4Å: Chain A: H.82, W.230 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.230 Water bridges: A:Q.84, A:Q.84, A:K.170 Salt bridges: A:H.82 SO4.5: 8 residues within 4Å: Chain A: K.117, R.120 Chain B: K.117, R.120 Chain C: K.117, R.120 Ligands: SO4.12, SO4.19 9 PLIP interactions: 4 interactions with chain A, 3 interactions with chain C, 2 interactions with chain B Water bridges: A:D.229, A:D.229, C:D.229 Salt bridges: A:K.117, A:R.120, C:K.117, C:R.120, B:K.117, B:R.120 SO4.6: 3 residues within 4Å: Chain A: Y.134, R.138, K.185 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.138, A:K.185 SO4.7: 3 residues within 4Å: Chain A: Q.37, Q.77, K.98 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.37, A:Q.77, A:Q.77 Water bridges: A:K.98, A:K.98 Salt bridges: A:K.98 SO4.10: 6 residues within 4Å: Chain B: H.44, K.185, G.186, S.188 Ligands: G0R.8, BEN.9 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.186, B:S.188 Water bridges: B:L.28 Salt bridges: B:H.44 SO4.11: 2 residues within 4Å: Chain B: H.82, W.230 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:W.230 Water bridges: B:Q.84, B:Q.84, B:K.170 Salt bridges: B:H.82 SO4.12: 8 residues within 4Å: Chain A: K.117, R.120 Chain B: K.117, R.120 Chain C: K.117, R.120 Ligands: SO4.5, SO4.19 9 PLIP interactions: 3 interactions with chain A, 3 interactions with chain C, 3 interactions with chain B Water bridges: A:D.229, C:D.229, B:D.229 Salt bridges: A:K.117, A:R.120, C:K.117, C:R.120, B:K.117, B:R.120 SO4.13: 3 residues within 4Å: Chain B: Y.134, R.138, K.185 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.134 Salt bridges: B:R.138, B:K.185 SO4.14: 3 residues within 4Å: Chain B: Q.37, Q.77, K.98 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.37, B:Q.77, B:Q.77 Water bridges: B:K.98, B:K.98 Salt bridges: B:K.98 SO4.17: 6 residues within 4Å: Chain C: H.44, K.185, G.186, S.188 Ligands: G0R.15, BEN.16 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.186, C:S.188, C:S.188 Salt bridges: C:H.44 SO4.18: 2 residues within 4Å: Chain C: H.82, W.230 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:W.230 Water bridges: C:Q.84, C:Q.84, C:K.170 Salt bridges: C:H.82 SO4.19: 8 residues within 4Å: Chain A: K.117, R.120 Chain B: K.117, R.120 Chain C: K.117, R.120 Ligands: SO4.5, SO4.12 9 PLIP interactions: 2 interactions with chain B, 4 interactions with chain C, 3 interactions with chain A Salt bridges: B:K.117, B:R.120, C:K.117, C:R.120, A:K.117, A:R.120 Water bridges: C:D.229, C:D.229, A:D.229 SO4.20: 3 residues within 4Å: Chain C: Y.134, R.138, K.185 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:R.138, C:K.185 SO4.21: 3 residues within 4Å: Chain C: Q.37, Q.77, K.98 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Q.37, C:Q.77, C:Q.77 Water bridges: C:K.98, C:K.98 Salt bridges: C:K.98

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Buchanan, M.S. et al., Clavatadine A, a natural product with selective recognition and irreversible inhibition of factor XIa. J.Med.Chem. (2008)

Release Date

2008-12-09

Peptides

Coagulation factor XIa light chain: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Coagulation factor XIa light chain

Related Entries With Identical Sequence