SMTL ID : 8ol9.1

Anti-FIXa Fab in complex with human des-(Gla-EGF1) FIXa

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: K.39, K.42, K.45 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:K.39, A:K.42, A:K.45 SO4.3: 4 residues within 4Å: Chain B: S.7, G.8, G.9, K.210 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.8, B:G.9

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.2: 4 residues within 4Å: Chain A: S.121, D.122, E.123 Chain B: K.223 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.122, A:D.122, A:E.123

1 x CA: CALCIUM ION(Non-covalent)

CA.4: 6 residues within 4Å: Chain C: E.55, N.57, I.58, E.60, E.62, E.65 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.55, C:N.57, C:E.60, C:E.62, C:E.62

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

0GJ.5: 14 residues within 4Å: Chain C: H.41, K.85, Y.86, D.179, S.180, C.181, Q.182, G.183, S.185, S.204, W.205, G.206, E.208, G.216 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Y.86, C:Q.182, C:G.183, C:S.185, C:S.185, C:E.208 Salt bridges: C:D.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Greisen, P.J. et al., Computational design of N-linked glycans for high throughput epitope profiling. Protein Sci. (2023)

Release Date

2023-07-19

Peptides

Light chain of FIXa binding Fab: A
Heavy chain of FIXa binding Fab: B
Coagulation factor IX heavy chain: C
Coagulation factor IX light chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
H

D
L

Light chain of FIXa binding Fab

Heavy chain of FIXa binding Fab

Coagulation factor IX heavy chain

Coagulation factor IX light chain

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