SMTL ID : 5da5.2 (2 other biounits)

Crystal structure of Rhodospirillum rubrum Rru_A0973

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

homo-10-mer

Ligands

10 x FE: FE (III) ION(Non-covalent)

FE.1: 7 residues within 4Å: Chain A: E.32, E.62, H.65 Chain J: Y.39, E.62 Ligands: FE.3, GOA.4 5 PLIP interactions: 3 interactions with chain A, 1 interactions with chain J, 1 Ligand-Ligand interactions Metal complexes: A:E.32, A:E.62, A:H.65, J:E.62, GOA.4 FE.3: 7 residues within 4Å: Chain A: Y.39, E.62 Chain J: E.32, E.62, H.65 Ligands: FE.1, GOA.4 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain J Metal complexes: A:E.62, J:E.32, J:E.32, J:E.62, J:H.65 FE.5: 7 residues within 4Å: Chain B: E.32, E.62, H.65 Chain C: Y.39, E.62 Ligands: GOA.6, FE.10 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Metal complexes: C:E.62, C:E.62, B:E.32, B:E.32, B:E.62 FE.10: 7 residues within 4Å: Chain B: Y.39, E.62 Chain C: E.32, E.62, H.65 Ligands: FE.5, GOA.6 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Metal complexes: C:E.32, C:E.32, C:E.62, C:H.65, B:E.62 FE.11: 7 residues within 4Å: Chain D: E.32, E.62, H.65 Chain E: Y.39, E.62 Ligands: GOA.12, FE.14 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain E Metal complexes: D:E.32, D:E.32, D:E.62, E:E.62, E:E.62 FE.14: 7 residues within 4Å: Chain D: Y.39, E.62 Chain E: E.32, E.62, H.65 Ligands: FE.11, GOA.12 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain E Metal complexes: D:E.62, D:E.62, E:E.32, E:E.32, E:E.62 FE.16: 7 residues within 4Å: Chain F: E.32, E.62, H.65 Chain H: Y.39, E.62 Ligands: GOA.17, FE.19 5 PLIP interactions: 2 interactions with chain H, 3 interactions with chain F Metal complexes: H:E.62, H:E.62, F:E.32, F:E.32, F:E.62 FE.19: 7 residues within 4Å: Chain F: Y.39, E.62 Chain H: E.32, E.62, H.65 Ligands: FE.16, GOA.17 5 PLIP interactions: 3 interactions with chain H, 2 interactions with chain F Metal complexes: H:E.32, H:E.32, H:E.62, F:E.62, F:E.62 FE.20: 7 residues within 4Å: Chain G: E.32, E.62, H.65 Chain I: Y.39, E.62 Ligands: FE.21, GOA.22 5 PLIP interactions: 3 interactions with chain G, 2 interactions with chain I Metal complexes: G:E.32, G:E.32, G:H.65, I:E.62, I:E.62 FE.21: 7 residues within 4Å: Chain G: Y.39, E.62 Chain I: E.32, E.62, H.65 Ligands: FE.20, GOA.22 5 PLIP interactions: 3 interactions with chain I, 1 interactions with chain G, 1 Ligand-Ligand interactions Metal complexes: I:E.32, I:E.62, I:H.65, G:E.62, GOA.22

8 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: E.31, E.34 Chain J: E.31, E.34 5 PLIP interactions: 2 interactions with chain J, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: J:E.31, J:E.34, A:E.31, H2O.1, H2O.10 CA.7: 5 residues within 4Å: Chain B: H.57, E.61 Chain C: E.61, E.64 Ligands: CA.8 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.61, H2O.2, H2O.4 CA.8: 4 residues within 4Å: Chain B: E.61, E.64 Chain C: E.61 Ligands: CA.7 No protein-ligand interaction detected (PLIP) CA.9: 5 residues within 4Å: Chain B: E.31, E.34 Chain C: E.31, E.34 Ligands: GOA.6 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: B:E.31, C:E.31, C:E.34, H2O.2, H2O.4 CA.13: 4 residues within 4Å: Chain D: E.31, E.34 Chain E: E.31, E.34 5 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: E:E.31, E:E.34, D:E.31, H2O.5, H2O.6 CA.15: 4 residues within 4Å: Chain D: W.72, N.76 Chain E: D.48, E.50 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.48, E:D.48 CA.18: 4 residues within 4Å: Chain F: E.31, E.34 Chain H: E.31, E.34 5 PLIP interactions: 2 interactions with chain H, 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: H:E.31, H:E.34, F:E.31, H2O.7, H2O.8 CA.23: 5 residues within 4Å: Chain G: E.31, E.34 Chain I: E.31, E.34 Ligands: GOA.22 5 PLIP interactions: 2 interactions with chain I, 1 interactions with chain G, 2 Ligand-Water interactions Metal complexes: I:E.31, I:E.34, G:E.31, H2O.7, H2O.9

5 x GOA: GLYCOLIC ACID(Non-covalent)

GOA.4: 11 residues within 4Å: Chain A: E.31, E.32, A.35, Y.39, E.62 Chain J: E.31, E.32, A.35, E.62 Ligands: FE.1, FE.3 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain J Hydrogen bonds: A:E.31 Water bridges: A:A.35, J:A.35 GOA.6: 12 residues within 4Å: Chain B: E.31, E.32, A.35, E.62 Chain C: E.31, E.32, A.35, Y.39, E.62 Ligands: FE.5, CA.9, FE.10 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:E.62, B:E.32 Water bridges: C:A.35, B:A.35 GOA.12: 11 residues within 4Å: Chain D: E.31, E.32, A.35, E.62 Chain E: E.31, E.32, A.35, Y.39, E.62 Ligands: FE.11, FE.14 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:E.62 Water bridges: E:A.35, D:A.35 GOA.17: 11 residues within 4Å: Chain F: E.31, E.32, A.35, E.62 Chain H: E.31, E.32, A.35, Y.39, E.62 Ligands: FE.16, FE.19 No protein-ligand interaction detected (PLIP) GOA.22: 12 residues within 4Å: Chain G: E.31, E.32, A.35, Y.39, E.62 Chain I: E.31, E.32, A.35, E.62 Ligands: FE.20, FE.21, CA.23 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:E.31 Water bridges: G:A.35, G:A.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

He, D. et al., Structural characterization of encapsulated ferritin provides insight into iron storage in bacterial nanocompartments. Elife (2016)

Release Date

2016-08-10

Peptides

Rru_A0973: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
K

B
L

C
M

D
N

E
O

F
P

G
Q

H
R

I
S

J
T

Rru_A0973

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