SMTL ID : 4kty.2 (1 other biounit)

Fibrin-stabilizing factor with a bound ligand

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

monomer

Ligands

1 x ACY- DAS- 1TX- ABA- NLE- LEU- PRO- TRP- PRO: Peptide-like ligand(Non-covalent)

ACY-DAS-1TX-ABA-NLE-LEU-PRO-TRP-PRO.1: 23 residues within 4Å: Chain A: Y.221, R.230, W.286, S.297, Q.320, C.321, W.322, F.346, M.357, I.359, T.372, D.374, S.375, V.376, W.377, N.378, Y.379, H.380, T.405, Q.407, L.446, Y.448, H.466 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:W.322, A:F.346, A:M.357, A:I.359, A:I.359, A:V.376, A:W.377, A:W.377, A:Y.379, A:L.446, A:L.446 Hydrogen bonds: A:Q.320, A:Q.320, A:C.321, A:V.376, A:N.378, A:N.378, A:N.378 Water bridges: A:R.230, A:R.230, A:Y.290, A:V.376 Salt bridges: A:R.230, A:H.380

3 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: A.271, N.274, A.275, K.276, D.278 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:A.271, A:N.274, A:K.276, A:D.278, A:D.278 CA.3: 6 residues within 4Å: Chain A: D.350, D.352, N.354, Q.356, D.358, D.374 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.350, A:D.352, A:Q.356, A:D.358, A:D.374 CA.4: 4 residues within 4Å: Chain A: N.443, A.464, E.492, E.497 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:A.464, A:E.492, A:E.497, H2O.3, H2O.16

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: Y.201, L.202, D.203, W.386, F.566, T.568 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.203, A:D.203, A:W.386, A:T.568 GOL.6: 5 residues within 4Å: Chain A: F.60, D.65, T.66, Y.90, R.150 4 PLIP interactions: 4 interactions with chain A Water bridges: A:D.65, A:D.65, A:T.66, A:T.66 GOL.7: 2 residues within 4Å: Chain A: R.107, W.171 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.107 Water bridges: A:F.106

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

SO4.8: 2 residues within 4Å: Chain A: K.276, D.277 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.277 Water bridges: A:E.279 Salt bridges: A:K.276

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stieler, M. et al., Structure of Active Coagulation Factor XIII Triggered by Calcium Binding: Basis for the Design of Next-Generation Anticoagulants. Angew.Chem.Int.Ed.Engl. (2013)

Release Date

2013-12-04

Peptides

Coagulation factor XIII A chain: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Coagulation factor XIII A chain

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