SMTL ID : 6mf0.1 (1 other biounit)

Crystal Structure Determination of Human/Porcine Chimera Coagulation Factor VIII

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

homo-dimer

Ligands

3 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.1: 5 residues within 4Å: Chain A: R.36, Q.248, V.258, N.259, H.336 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.3: 7 residues within 4Å: Chain A: L.887, R.1004, V.1006, Q.1073, K.1154, N.1253, N.1276 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.1006 NAG-NAG-BMA-MAN-MAN.4: 3 residues within 4Å: Chain B: R.36, V.258, N.259 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.2: 3 residues within 4Å: Chain A: K.911, Q.913, N.945 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- NAG- MAN- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-NAG-MAN-FUC.5: 3 residues within 4Å: Chain B: K.911, Q.913, N.945 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN.6: 9 residues within 4Å: Chain B: L.887, H.1002, R.1004, V.1006, T.1007, Q.1073, N.1253, N.1276, P.1277 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.1073, B:Q.1073

2 x CA: CALCIUM ION(Non-covalent)

CA.7: 6 residues within 4Å: Chain A: K.127, E.130, A.132, E.142, D.145, D.146 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:K.127, A:E.142, A:D.145, A:D.145, A:D.146 CA.10: 5 residues within 4Å: Chain B: K.127, D.136, E.142, D.145, D.146 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:K.127, B:E.142, B:D.145, B:D.146, B:D.146

2 x ZN: ZINC ION(Non-covalent)

ZN.8: 4 residues within 4Å: Chain A: H.287, C.330, H.337, M.340 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.287, A:C.330, A:H.337 ZN.11: 5 residues within 4Å: Chain B: H.252, V.286, H.287, C.330, H.337 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.287, B:C.330, B:H.337, B:H.337

2 x CU1: COPPER (I) ION(Non-covalent)

CU1.9: 4 residues within 4Å: Chain A: H.1089, C.1135, H.1140, M.1145 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.1089, A:C.1135, A:H.1140 CU1.12: 5 residues within 4Å: Chain B: I.1088, H.1089, C.1135, H.1140, M.1145 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.1089, B:C.1135, B:H.1140

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Smith, I.W. et al., The 3.2 angstrom structure of a bioengineered variant of blood coagulation factor VIII indicates two conformations of the C2 domain. J.Thromb.Haemost. (2020)

Release Date

2019-09-11

Peptides

Coagulation factor VIII chimera: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Coagulation factor VIII chimera

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