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

Fibrin-stabilizing factor with a bound ligand

Coordinates

PDB Format Compare

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: 22 residues within 4Å: Chain A: Y.221, W.286, Y.290, 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, L.446, Y.448, H.466 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:W.322, A:F.346, A:M.357, A:I.359, A:V.376, A:W.377, A:N.378, 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:V.376 Salt bridges: 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.1, H2O.1

6 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 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.203, A:D.203, A:W.386, A:T.568 Water bridges: A:T.568 GOL.6: 5 residues within 4Å: Chain A: F.60, D.65, T.66, Y.90, R.150 9 PLIP interactions: 9 interactions with chain A Water bridges: A:D.65, A:D.65, A:D.65, A:T.66, A:T.66, A:T.66, A:N.67, A:N.67, A:R.150 GOL.7: 5 residues within 4Å: Chain A: V.294, E.308, P.315, V.316, R.317 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:P.315, A:R.317 Water bridges: A:E.308, A:R.317, A:R.317 GOL.8: 6 residues within 4Å: Chain A: N.27, E.30, K.163, R.165, R.181, D.186 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.27, A:V.111, A:K.163, A:R.165, A:R.181, A:D.186, A:D.186 Water bridges: A:K.163 GOL.9: 2 residues within 4Å: Chain A: R.722, H.723 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.722, A:H.723 GOL.10: 5 residues within 4Å: Chain A: N.548, N.549, L.587, S.588, F.589 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.549

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
A

Coagulation factor XIII A chain

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