SMTL ID : 6aod.1

FXIa antibody complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

SO4.1: 9 residues within 4Å: Chain A: D.32, G.34, Y.36, R.46, Y.49, L.89, H.91 Chain B: L.99 Chain C: R.138 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:Y.36 Water bridges: A:D.32, C:R.138 Salt bridges: A:R.46, A:H.91, C:R.138 SO4.7: 2 residues within 4Å: Chain B: R.85, R.87 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.85, B:R.87 SO4.8: 4 residues within 4Å: Chain B: R.98, F.103, R.104, Y.106 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.104 Water bridges: B:R.98 Salt bridges: B:R.98 SO4.9: 6 residues within 4Å: Chain B: Y.33, H.35, L.99, A.100, S.101 Chain C: R.138 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Y.33, B:L.99, B:S.101 Water bridges: B:A.100, B:A.100 Salt bridges: B:H.35, C:R.138

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: D.92, I.93, Y.94, A.95 Chain C: R.26 6 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: A:Y.94, A:A.95, C:R.26 Water bridges: A:Q.90, A:A.95, B:Q.62 GOL.3: 1 residues within 4Å: Chain A: R.24 No protein-ligand interaction detected (PLIP) GOL.4: 5 residues within 4Å: Chain A: S.121, D.122, E.123 Chain B: P.127, K.213 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.122, A:D.122, A:E.123, B:K.213 GOL.11: 4 residues within 4Å: Chain B: T.58, Y.60, Q.65, T.69 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.60, B:Y.60, B:Q.65, B:Q.65 GOL.17: 3 residues within 4Å: Chain C: Q.63, N.143, T.144 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:N.143, C:N.143, C:T.144, C:T.144, C:T.144 Water bridges: C:Q.146 GOL.18: 10 residues within 4Å: Chain C: S.7, V.8, G.10, E.11, W.12, G.60, I.61, L.62, S.108, L.145 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.10, C:E.11, C:W.12, C:I.61, C:S.108 GOL.19: 5 residues within 4Å: Chain C: F.74, T.102, V.103, Q.104, Q.109 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.102, C:Q.104, C:Q.109 Water bridges: C:Q.104 GOL.20: 1 residues within 4Å: Chain C: S.51 No protein-ligand interaction detected (PLIP) GOL.21: 3 residues within 4Å: Chain C: K.136, L.137, R.138 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:L.137, C:R.138, C:Q.214 Water bridges: C:R.138

3 x CO: COBALT (II) ION(Non-covalent)

CO.5: 2 residues within 4Å: Chain B: N.203, K.205 No protein-ligand interaction detected (PLIP) CO.6: 2 residues within 4Å: Chain B: S.7, G.8 No protein-ligand interaction detected (PLIP) CO.12: 1 residues within 4Å: Chain C: Y.105 No protein-ligand interaction detected (PLIP)

5 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.10: 3 residues within 4Å: Chain B: Y.27, T.28, Y.32 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.28, B:T.28, B:Y.32 Water bridges: B:R.98 PO4.13: 3 residues within 4Å: Chain C: D.70, T.71, S.72 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.72 PO4.14: 2 residues within 4Å: Chain C: T.24, Q.25 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.24, C:T.24, C:Q.25 PO4.15: 2 residues within 4Å: Chain C: K.149, Y.176 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Y.176 Water bridges: C:K.149, C:K.149, C:Y.176 Salt bridges: C:K.149 PO4.16: 2 residues within 4Å: Chain C: T.168, H.169 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.169 Salt bridges: C:H.169

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ely, L.K. et al., Structural Basis for Activity and Specificity of an Anticoagulant Anti-FXIa Monoclonal Antibody and a Reversal Agent. Structure (2018)

Release Date

2018-03-14

Peptides

FXIa Antibody FAB Light Chain: A
FXIa Antibody FAB Heavy Chain: B
Coagulation factor XI: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

FXIa Antibody FAB Light Chain

FXIa Antibody FAB Heavy Chain

Coagulation factor XI