SMTL ID : 1nl0.2 (1 other biounit)

Crystal structure of human factor IX Gla domain in complex of an inhibitory antibody, 10C12

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-2-2-2-mer

Ligands

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

SO4.1: 8 residues within 4Å: Chain A: E.84, V.109, G.111, Q.112, Y.144, K.170, N.174 Chain D: S.81 9 PLIP interactions: 2 interactions with chain D, 7 interactions with chain A Hydrogen bonds: D:S.81, D:S.81, A:E.84, A:G.111, A:Q.112, A:N.174 Water bridges: A:K.170, A:K.170 Salt bridges: A:K.170 SO4.8: 8 residues within 4Å: Chain A: S.81 Chain D: E.84, V.109, G.111, Q.112, Y.144, K.170, N.174 11 PLIP interactions: 9 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:E.84, D:G.111, D:Q.112, D:Y.144, D:N.174, A:S.81, A:S.81 Water bridges: D:K.170, D:K.170, D:Y.176 Salt bridges: D:K.170

12 x CA: CALCIUM ION(Non-covalent)

CA.2: 3 residues within 4Å: Chain C: E.26, E.30 Ligands: CA.3 No protein-ligand interaction detected (PLIP) CA.3: 4 residues within 4Å: Chain C: E.8, E.27, E.30 Ligands: CA.2 No protein-ligand interaction detected (PLIP) CA.4: 5 residues within 4Å: Chain C: E.8, E.17, E.27, E.30 Ligands: CA.5 No protein-ligand interaction detected (PLIP) CA.5: 8 residues within 4Å: Chain C: Y.1, N.2, E.7, E.8, E.17, E.27 Ligands: CA.4, CA.6 No protein-ligand interaction detected (PLIP) CA.6: 5 residues within 4Å: Chain C: Y.1, E.7, E.17, E.21 Ligands: CA.5 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:Y.1, H2O.6 CA.7: 2 residues within 4Å: Chain C: E.15, E.20 No protein-ligand interaction detected (PLIP) CA.9: 3 residues within 4Å: Chain F: E.26, E.30 Ligands: CA.10 No protein-ligand interaction detected (PLIP) CA.10: 4 residues within 4Å: Chain F: E.8, E.27, E.30 Ligands: CA.9 No protein-ligand interaction detected (PLIP) CA.11: 5 residues within 4Å: Chain F: E.8, E.17, E.27, E.30 Ligands: CA.12 No protein-ligand interaction detected (PLIP) CA.12: 8 residues within 4Å: Chain F: Y.1, N.2, E.7, E.8, E.17, E.27 Ligands: CA.11, CA.13 No protein-ligand interaction detected (PLIP) CA.13: 5 residues within 4Å: Chain F: Y.1, E.7, E.17, E.21 Ligands: CA.12 2 PLIP interactions: 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:Y.1, H2O.12 CA.14: 2 residues within 4Å: Chain F: E.15, E.20 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, M. et al., Crystal Structure of the Calcium-stabilized Human Factor IX Gla Domain Bound to a Conformation-specific Anti-factor IX Antibody. J.Biol.Chem. (2004)

Release Date

2004-01-20

Peptides

anti-factor IX antibody, 10C12, chain L: AD
anti-factor IX antibody, 10C12, chain H: BE
factor IX: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

D
L

B
H

E
H

C
G

F
G

anti-factor IX antibody, 10C12, chain L

anti-factor IX antibody, 10C12, chain H

factor IX

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