SMTL ID : 3m7p.1

Fibronectin fragment

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

6 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 4 residues within 4Å: Chain A: P.127, L.129, N.132, N.134 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.129 NAG.2: 3 residues within 4Å: Chain A: N.232, D.233, V.287 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.232 NAG.3: 4 residues within 4Å: Chain A: Q.221, I.223, N.246, D.260 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.223 Hydrogen bonds: A:Q.221 NAG.13: 4 residues within 4Å: Chain B: P.127, L.129, N.132, N.134 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.129 NAG.14: 3 residues within 4Å: Chain B: N.232, D.233, V.287 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.232 NAG.15: 4 residues within 4Å: Chain B: Q.221, I.223, N.246, D.260 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.223 Hydrogen bonds: B:Q.221, B:D.260

14 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: E.171, R.207, D.233, H.236 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.171, A:E.171, A:D.233, A:D.233, A:H.236 ZN.5: 3 residues within 4Å: Chain A: R.73, H.239, H.302 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.239, A:H.302, H2O.2 ZN.6: 4 residues within 4Å: Chain A: D.85, H.87 Chain B: D.226, H.243 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:D.226, B:D.226, B:H.243, A:H.87, H2O.1 ZN.7: 4 residues within 4Å: Chain A: H.170, E.172 Chain B: H.108, D.137 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Metal complexes: B:H.108, B:D.137, A:H.170, A:E.172, A:E.172 ZN.8: 2 residues within 4Å: Chain A: H.3, H.11 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.3, A:H.11, H2O.1 ZN.9: 3 residues within 4Å: Chain A: E.178, H.192, H.285 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.178, A:E.178, A:H.192, A:H.285 ZN.10: 3 residues within 4Å: Chain A: E.241, H.243, E.300 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:E.241, H2O.2, H2O.2, H2O.2, H2O.2, H2O.2 ZN.16: 4 residues within 4Å: Chain B: E.171, R.207, D.233, H.236 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.171, B:E.171, B:D.233, B:D.233, B:H.236 ZN.17: 3 residues within 4Å: Chain B: R.73, H.239, H.302 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.239, B:H.302, H2O.4 ZN.18: 4 residues within 4Å: Chain A: D.226, H.243 Chain B: D.85, H.87 5 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:D.226, A:D.226, A:H.243, B:H.87, H2O.3 ZN.19: 4 residues within 4Å: Chain A: H.108, D.137 Chain B: H.170, E.172 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Metal complexes: B:H.170, B:E.172, B:E.172, A:H.108, A:D.137 ZN.20: 2 residues within 4Å: Chain B: H.3, H.11 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.3, B:H.11, H2O.3 ZN.21: 3 residues within 4Å: Chain B: E.178, H.192, H.285 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.178, B:E.178, B:H.192, B:H.285 ZN.22: 3 residues within 4Å: Chain B: E.241, H.243, E.300 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:E.241, H2O.4, H2O.4, H2O.4, H2O.4, H2O.4

4 x 12P: DODECAETHYLENE GLYCOL(Non-covalent)

12P.11: 12 residues within 4Å: Chain A: Y.70, E.81, R.83, H.87, W.89, Y.96, Y.102, F.104 Chain B: I.213, V.224, D.226, L.245 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.104, B:I.213 Hydrogen bonds: A:R.83, A:R.83 Water bridges: B:D.226 12P.12: 1 residues within 4Å: Chain A: Q.290 No protein-ligand interaction detected (PLIP) 12P.23: 12 residues within 4Å: Chain A: I.213, V.224, D.226, L.245 Chain B: Y.70, E.81, R.83, H.87, W.89, Y.96, Y.102, F.104 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.104, A:I.213 Hydrogen bonds: B:R.83, B:R.83, B:Y.96, B:Y.102 Water bridges: A:D.226 12P.24: 1 residues within 4Å: Chain B: Q.290 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Graille, M. et al., Zinc Induces Structural Reorganization of Gelatin Binding Domain from Human Fibronectin and Affects Collagen Binding. Structure (2010)

Release Date

2010-06-23

Peptides

FN1 protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

FN1 protein