SMTL ID : 6h1c.1

Structure of Ferric uptake regulator from Pseudomonas aeruginosa with manganese.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.34 Å

Oligo State

homo-tetramer

Ligands

22 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 4 residues within 4Å: Chain A: H.32, E.80, H.89, E.100 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.32, A:E.80, A:E.80, A:H.89, A:E.100 MN.2: 2 residues within 4Å: Chain A: D.88, E.107 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.88, A:E.107, A:E.107, H2O.1, H2O.2 MN.3: 7 residues within 4Å: Chain A: S.34, A.35, E.36 Chain D: D.73, G.75, H.76 Ligands: MN.4 No protein-ligand interaction detected (PLIP) MN.4: 4 residues within 4Å: Chain A: E.36 Chain D: D.73, H.76 Ligands: MN.3 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D Metal complexes: A:E.36, D:D.73, D:H.76 MN.5: 3 residues within 4Å: Chain A: E.105 Chain B: E.105 Ligands: MN.17 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:E.105, B:E.105, H2O.2 MN.6: 5 residues within 4Å: Chain A: D.73, H.76 Chain D: E.36 Ligands: MN.36, MN.37 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Metal complexes: A:D.73, A:H.76, D:E.36 MN.7: 2 residues within 4Å: Chain A: H.70 Ligands: MN.8 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.70, H2O.2, H2O.2 MN.8: 3 residues within 4Å: Chain A: H.70, N.71 Ligands: MN.7 No protein-ligand interaction detected (PLIP) MN.13: 4 residues within 4Å: Chain B: H.32, E.80, H.89, E.100 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:H.32, B:E.80, B:E.80, B:H.89, B:E.100 MN.14: 2 residues within 4Å: Chain B: D.88, E.107 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.88, B:E.107, B:E.107, H2O.3, H2O.4 MN.15: 7 residues within 4Å: Chain B: S.34, A.35, E.36 Chain C: D.73, G.75, H.76 Ligands: MN.16 No protein-ligand interaction detected (PLIP) MN.16: 4 residues within 4Å: Chain B: E.36 Chain C: D.73, H.76 Ligands: MN.15 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Metal complexes: C:D.73, C:H.76, B:E.36 MN.17: 3 residues within 4Å: Chain A: E.105 Chain B: E.105 Ligands: MN.5 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:E.105, A:E.105, H2O.4 MN.18: 5 residues within 4Å: Chain B: D.73, H.76 Chain C: E.36 Ligands: MN.25, MN.26 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Metal complexes: B:D.73, B:H.76, C:E.36 MN.19: 2 residues within 4Å: Chain B: H.70 Ligands: MN.20 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.70, H2O.4, H2O.5 MN.20: 3 residues within 4Å: Chain B: H.70, N.71 Ligands: MN.19 No protein-ligand interaction detected (PLIP) MN.25: 6 residues within 4Å: Chain B: D.73, G.75, H.76 Chain C: E.36 Ligands: MN.18, MN.26 No protein-ligand interaction detected (PLIP) MN.26: 5 residues within 4Å: Chain B: D.73, H.76 Chain C: E.36 Ligands: MN.18, MN.25 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Metal complexes: B:D.73, B:D.73, B:H.76, C:E.36 MN.27: 7 residues within 4Å: Chain C: E.105, R.109 Chain D: E.105, R.109 Ligands: ZN.28, MN.38, ZN.39 No protein-ligand interaction detected (PLIP) MN.36: 6 residues within 4Å: Chain A: D.73, G.75, H.76 Chain D: E.36 Ligands: MN.6, MN.37 No protein-ligand interaction detected (PLIP) MN.37: 5 residues within 4Å: Chain A: D.73, H.76 Chain D: E.36 Ligands: MN.6, MN.36 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Metal complexes: A:D.73, A:D.73, A:H.76, D:E.36 MN.38: 7 residues within 4Å: Chain C: E.105, R.109 Chain D: E.105, R.109 Ligands: MN.27, ZN.28, ZN.39 No protein-ligand interaction detected (PLIP)

24 x ZN: ZINC ION(Non-covalent)

ZN.9: 3 residues within 4Å: Chain A: V.2, E.3, N.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.3 ZN.10: 5 residues within 4Å: Chain A: H.87, D.123, A.124, N.125 Ligands: ZN.11 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.87, A:D.123 ZN.11: 3 residues within 4Å: Chain A: H.87, D.123 Ligands: ZN.10 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.123 ZN.12: 4 residues within 4Å: Chain A: E.29, E.80, D.83, E.100 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.83, A:D.83 ZN.21: 3 residues within 4Å: Chain B: V.2, E.3, N.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.3 ZN.22: 5 residues within 4Å: Chain B: H.87, D.123, A.124, N.125 Ligands: ZN.23 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.87, B:D.123 ZN.23: 3 residues within 4Å: Chain B: H.87, D.123 Ligands: ZN.22 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.123 ZN.24: 4 residues within 4Å: Chain B: E.29, E.80, D.83, E.100 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.83, B:D.83 ZN.28: 5 residues within 4Å: Chain C: E.105 Chain D: E.105 Ligands: MN.27, MN.38, ZN.39 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.105 ZN.29: 5 residues within 4Å: Chain C: R.31, H.32, E.80, H.89, E.100 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:H.32, C:E.80, C:E.80, C:H.89, C:E.100 ZN.30: 3 residues within 4Å: Chain C: H.70, N.125 Ligands: ZN.31 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.70 ZN.31: 3 residues within 4Å: Chain C: H.70, N.71 Ligands: ZN.30 No protein-ligand interaction detected (PLIP) ZN.32: 3 residues within 4Å: Chain C: M.1, E.3, D.26 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.3, C:D.26 ZN.33: 2 residues within 4Å: Chain C: D.88, E.107 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.88, C:E.107, H2O.5, H2O.5, H2O.7 ZN.34: 3 residues within 4Å: Chain C: H.87, D.123 Ligands: ZN.35 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.123 ZN.35: 5 residues within 4Å: Chain C: H.87, D.123, A.124, N.125 Ligands: ZN.34 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.87, C:D.123 ZN.39: 5 residues within 4Å: Chain C: E.105 Chain D: E.105 Ligands: MN.27, ZN.28, MN.38 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.105 ZN.40: 5 residues within 4Å: Chain D: R.31, H.32, E.80, H.89, E.100 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:H.32, D:E.80, D:E.80, D:H.89, D:E.100 ZN.41: 3 residues within 4Å: Chain D: H.70, N.125 Ligands: ZN.42 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:H.70 ZN.42: 3 residues within 4Å: Chain D: H.70, N.71 Ligands: ZN.41 No protein-ligand interaction detected (PLIP) ZN.43: 3 residues within 4Å: Chain D: M.1, E.3, D.26 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.3, D:D.26 ZN.44: 2 residues within 4Å: Chain D: D.88, E.107 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.88, D:E.107, H2O.7, H2O.7, H2O.9 ZN.45: 3 residues within 4Å: Chain D: H.87, D.123 Ligands: ZN.46 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.123 ZN.46: 5 residues within 4Å: Chain D: H.87, D.123, A.124, N.125 Ligands: ZN.45 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:H.87, D:D.123

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nader, S. et al., Ferric uptake regulator with Mn and Zn form Pseudomonas aeruginosa. To Be Published

Release Date

2019-07-31

Peptides

Ferric uptake regulation protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
B

D
B

Ferric uptake regulation protein