SMTL ID : 9ghl.1

Fe(II)-2-oxoglutarate-dependent pseudomonal iron uptake factor C in complex with malate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-hexamer

Ligands

6 x MLT: D-MALATE(Non-covalent)

MLT.1: 9 residues within 4Å: Chain A: N.84, Y.86, F.92, H.95, T.117, H.158, V.160, R.168, F.172 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.84, A:Y.86 Water bridges: A:Y.86, A:H.158 Salt bridges: A:H.95, A:H.158, A:R.168 MLT.4: 9 residues within 4Å: Chain B: N.84, Y.86, F.92, H.95, T.117, H.158, V.160, R.168, F.172 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.84, B:Y.86 Water bridges: B:Y.86 Salt bridges: B:H.95, B:H.158, B:R.168 MLT.6: 9 residues within 4Å: Chain C: N.84, Y.86, F.92, H.95, T.117, H.158, V.160, R.168, F.172 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:N.84, C:Y.86 Water bridges: C:N.42, C:Y.86, C:Y.152 Salt bridges: C:H.95, C:H.158, C:R.168 MLT.8: 9 residues within 4Å: Chain D: N.84, Y.86, F.92, H.95, T.117, H.158, V.160, R.168, F.172 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:N.84, D:Y.86, D:Y.86, D:T.117 Water bridges: D:Y.86 Salt bridges: D:H.95, D:H.158, D:R.168 MLT.11: 9 residues within 4Å: Chain E: N.84, Y.86, F.92, H.95, T.117, H.158, V.160, R.168, F.172 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:N.84, E:Y.86, E:Y.86, E:T.117 Water bridges: E:Y.86 Salt bridges: E:H.95, E:H.158, E:R.168 MLT.13: 9 residues within 4Å: Chain F: N.84, Y.86, F.92, H.95, T.117, H.158, V.160, R.168, F.172 9 PLIP interactions: 9 interactions with chain F Hydrophobic interactions: F:V.160 Hydrogen bonds: F:N.84, F:Y.86, F:Y.86, F:T.117 Water bridges: F:Y.86 Salt bridges: F:H.95, F:H.158, F:R.168

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: Q.184, R.221, W.222 Chain E: Q.184, R.221, W.222 6 PLIP interactions: 3 interactions with chain E, 3 interactions with chain A Hydrogen bonds: E:Q.184, E:R.221, E:R.221, A:Q.184, A:R.221, A:R.221 GOL.9: 6 residues within 4Å: Chain B: Q.184, R.221, W.222 Chain D: Q.184, R.221, W.222 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:Q.184, B:R.221, B:R.221, D:Q.184, D:R.221, D:R.221 GOL.14: 6 residues within 4Å: Chain C: Q.184, R.221, W.222 Chain F: Q.184, R.221, W.222 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain F Hydrogen bonds: C:Q.184, C:R.221, C:R.221, F:Q.184, F:R.221, F:R.221

6 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 7 residues within 4Å: Chain A: F.8, E.12, R.15, E.54, I.55, A.58, R.62 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.15, A:R.15, A:R.62 PEG.5: 4 residues within 4Å: Chain B: F.8, R.15, A.58, R.62 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.15, B:R.15, B:R.62 PEG.7: 4 residues within 4Å: Chain C: F.8, E.12, A.58, R.62 No protein-ligand interaction detected (PLIP) PEG.10: 4 residues within 4Å: Chain D: F.8, I.16, E.54, I.55 No protein-ligand interaction detected (PLIP) PEG.12: 4 residues within 4Å: Chain E: F.8, E.54, I.55, A.58 No protein-ligand interaction detected (PLIP) PEG.15: 4 residues within 4Å: Chain F: I.16, A.19, E.54, I.55 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Alshref, F.M. et al., Fe(II)-2-oxoglutarate-dependent pseudomonal iron uptake factor C in complex with malate. To Be Published

Release Date

2025-08-27

Peptides

PKHD-type hydroxylase PiuC: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

PKHD-type hydroxylase PiuC