SMTL ID : 1xaf.1

Crystal Structure of Protein of Unknown Function YfiH from Shigella flexneri 2a str. 2457T

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

homo-dimer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.74, C.110, H.127 Ligands: ACT.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.74, A:C.110, A:H.127 ZN.2: 1 residues within 4Å: Chain A: H.49 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.49 ZN.3: 3 residues within 4Å: Chain A: C.219, T.222 Ligands: ACT.7 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:C.219, A:T.222, ACT.7 ZN.4: 1 residues within 4Å: Chain A: H.189 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.189, H2O.6 ZN.5: 2 residues within 4Å: Chain A: H.42 Chain B: H.189 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:H.189, A:H.42, H2O.10, H2O.14 ZN.9: 4 residues within 4Å: Chain B: H.74, C.110, H.127 Ligands: ACT.12 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.74, B:C.110, B:H.127 ZN.10: 1 residues within 4Å: Chain B: H.49 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.49 ZN.11: 4 residues within 4Å: Chain B: C.219, T.222 Ligands: ACT.13, ACT.14 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Ligand interactions Metal complexes: B:C.219, B:T.222, ACT.13, ACT.14

5 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 8 residues within 4Å: Chain A: H.74, T.107, A.108, D.109, C.110, H.127, R.238 Ligands: ZN.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.108 Hydrogen bonds: A:A.108, A:C.110 Salt bridges: A:H.74, A:H.127 ACT.7: 6 residues within 4Å: Chain A: G.161, P.162, R.163, C.219, T.222 Ligands: ZN.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.162 Hydrogen bonds: A:G.161, A:R.163, A:A.164 Salt bridges: A:R.163 ACT.12: 9 residues within 4Å: Chain B: H.74, T.107, A.108, D.109, C.110, H.127, Y.230, R.238 Ligands: ZN.9 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.230 Hydrogen bonds: B:A.108, B:C.110 Salt bridges: B:H.74, B:H.127 ACT.13: 7 residues within 4Å: Chain A: H.42 Chain B: R.163, A.164, C.219, T.222 Ligands: ZN.11, ACT.14 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:R.163, B:A.164, A:H.42 ACT.14: 8 residues within 4Å: Chain B: G.161, P.162, R.163, A.164, C.219, T.222 Ligands: ZN.11, ACT.13 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:R.163 Hydrogen bonds: B:G.161, B:R.163, B:A.164 Salt bridges: B:R.163

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 5 residues within 4Å: Chain A: G.40, A.41, H.42, R.54, M.106 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.41, A:H.42, A:R.54 GOL.15: 7 residues within 4Å: Chain B: L.39, G.40, A.41, H.42, C.43, R.54, M.106 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.39, B:A.41, B:H.42

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Crystal structure of hypothetical protein YfiH from Shigella flexneri at 2 A resolution. Proteins (2006)

Release Date

2004-08-31

Peptides

orf, conserved hypothetical protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

orf, conserved hypothetical protein