SMTL ID : 9qg1.1

Natively purified Rubrerythrin 16-mer from the anaerobic extremophile P. furiosus

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-16-mer

Ligands

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

FE.1: 4 residues within 4Å: Chain A: C.142, C.145, C.157, C.160 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.142, A:C.145, A:C.157, A:C.160 FE.2: 5 residues within 4Å: Chain A: E.80, E.114, H.117 Chain B: E.52 Ligands: FE.3 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Metal complexes: A:E.80, A:E.80, A:E.114, A:H.117, B:E.52 FE.3: 6 residues within 4Å: Chain A: E.80, E.83, E.114 Chain B: Y.26, E.52 Ligands: FE.2 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Metal complexes: A:E.80, A:E.83, A:E.114, B:E.52, B:E.52 FE.4: 5 residues within 4Å: Chain B: C.142, I.144, C.145, C.157, C.160 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.145, B:C.157, B:C.160 FE.5: 5 residues within 4Å: Chain A: E.52 Chain B: E.80, E.114, H.117 Ligands: FE.6 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Metal complexes: B:E.80, B:E.80, B:E.114, B:H.117, A:E.52 FE.6: 5 residues within 4Å: Chain A: E.19, E.52 Chain B: E.83, E.114 Ligands: FE.5 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Metal complexes: B:E.83, B:E.83, B:E.114, A:E.19, A:E.52 FE.7: 4 residues within 4Å: Chain C: C.142, C.145, C.157, C.160 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.142, C:C.145, C:C.157, C:C.160 FE.8: 5 residues within 4Å: Chain C: E.80, E.83, E.114 Chain D: E.52 Ligands: FE.9 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Metal complexes: C:E.80, C:E.83, C:E.114, C:E.114, D:E.52 FE.9: 6 residues within 4Å: Chain C: E.80, H.117 Chain D: Y.26, I.48, E.52 Ligands: FE.8 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Metal complexes: D:Y.26, D:E.52, C:E.80 FE.10: 4 residues within 4Å: Chain D: C.142, C.145, C.157, C.160 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.142, D:C.145, D:C.157, D:C.160 FE.11: 6 residues within 4Å: Chain C: E.52 Chain D: E.80, E.83, E.114, H.117 Ligands: FE.12 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.80, D:E.83, D:E.114, D:E.114 FE.12: 5 residues within 4Å: Chain C: E.19, E.52 Chain D: E.83, E.114 Ligands: FE.11 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Metal complexes: C:E.19, C:E.19, D:E.83, D:E.83, D:E.114 FE.13: 4 residues within 4Å: Chain E: C.142, C.145, C.157, C.160 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.142, E:C.145, E:C.157, E:C.160 FE.14: 5 residues within 4Å: Chain E: E.80, E.114, H.117 Chain F: E.52 Ligands: FE.15 5 PLIP interactions: 1 interactions with chain F, 4 interactions with chain E Metal complexes: F:E.52, E:E.80, E:E.80, E:E.114, E:H.117 FE.15: 6 residues within 4Å: Chain E: E.80, E.83, E.114 Chain F: E.19, E.52 Ligands: FE.14 5 PLIP interactions: 2 interactions with chain F, 3 interactions with chain E Metal complexes: F:E.52, F:E.52, E:E.83, E:E.114, E:E.114 FE.16: 4 residues within 4Å: Chain F: C.142, C.145, C.157, C.160 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:C.142, F:C.145, F:C.157 FE.17: 6 residues within 4Å: Chain E: E.52 Chain F: E.80, E.83, E.114, H.117 Ligands: FE.18 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain F Metal complexes: E:E.52, E:E.52, F:E.80, F:E.80, F:E.114 FE.18: 5 residues within 4Å: Chain E: E.19, E.52 Chain F: E.83, E.114 Ligands: FE.17 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain F Metal complexes: E:E.19, E:E.19, F:E.83, F:E.83, F:E.114 FE.19: 3 residues within 4Å: Chain G: C.142, C.145, C.157 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:C.142, G:C.145, G:C.157 FE.20: 5 residues within 4Å: Chain G: E.80, E.83, E.114 Chain H: E.52 Ligands: FE.22 5 PLIP interactions: 1 interactions with chain H, 4 interactions with chain G Metal complexes: H:E.52, G:E.80, G:E.83, G:E.114, G:E.114 FE.21: 6 residues within 4Å: Chain G: E.19, E.52 Chain H: E.83, Y.88, E.114 Ligands: FE.24 5 PLIP interactions: 2 interactions with chain H, 3 interactions with chain G Metal complexes: H:E.83, H:E.114, G:E.19, G:E.19, G:E.52 FE.22: 6 residues within 4Å: Chain G: E.80, H.117 Chain H: Y.26, I.48, E.52 Ligands: FE.20 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain G Metal complexes: H:E.52, G:E.80 FE.23: 4 residues within 4Å: Chain H: C.142, C.145, C.157, C.160 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.142, H:C.145, H:C.157, H:C.160 FE.24: 6 residues within 4Å: Chain G: E.52 Chain H: E.80, E.83, E.114, H.117 Ligands: FE.21 5 PLIP interactions: 3 interactions with chain H, 2 interactions with chain G Metal complexes: H:E.80, H:E.114, H:E.114, G:E.52, G:E.52 FE.25: 4 residues within 4Å: Chain I: C.142, C.145, C.157, C.160 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.142, I:C.145, I:C.157, I:C.160 FE.26: 6 residues within 4Å: Chain I: E.80, E.83, E.114, H.117 Chain J: E.52 Ligands: FE.27 5 PLIP interactions: 4 interactions with chain I, 1 interactions with chain J Metal complexes: I:E.80, I:E.83, I:E.114, I:E.114, J:E.52 FE.27: 6 residues within 4Å: Chain I: E.83, E.114 Chain J: E.19, A.22, E.52 Ligands: FE.26 3 PLIP interactions: 2 interactions with chain I, 1 interactions with chain J Metal complexes: I:E.83, I:E.83, J:E.52 FE.28: 4 residues within 4Å: Chain J: C.142, C.145, C.157, C.160 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.142, J:C.145, J:C.157, J:C.160 FE.29: 6 residues within 4Å: Chain I: E.52 Chain J: E.80, E.83, E.114, H.117 Ligands: FE.30 5 PLIP interactions: 4 interactions with chain J, 1 interactions with chain I Metal complexes: J:E.80, J:E.80, J:E.114, J:H.117, I:E.52 FE.30: 6 residues within 4Å: Chain I: E.19, E.52 Chain J: E.80, E.83, E.114 Ligands: FE.29 5 PLIP interactions: 2 interactions with chain I, 3 interactions with chain J Metal complexes: I:E.52, I:E.52, J:E.83, J:E.114, J:E.114 FE.31: 5 residues within 4Å: Chain K: C.142, I.144, C.145, C.157, C.160 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:C.145, K:C.157, K:C.160 FE.32: 6 residues within 4Å: Chain K: E.80, E.83, E.114 Chain L: E.19, E.52 Ligands: FE.34 5 PLIP interactions: 4 interactions with chain K, 1 interactions with chain L Metal complexes: K:E.80, K:E.83, K:E.114, K:E.114, L:E.52 FE.33: 5 residues within 4Å: Chain K: E.19, E.52 Chain L: E.83, E.114 Ligands: FE.36 5 PLIP interactions: 3 interactions with chain L, 2 interactions with chain K Metal complexes: L:E.83, L:E.83, L:E.114, K:E.19, K:E.52 FE.34: 5 residues within 4Å: Chain K: E.80, E.114, H.117 Chain L: E.52 Ligands: FE.32 5 PLIP interactions: 4 interactions with chain K, 1 interactions with chain L Metal complexes: K:E.80, K:E.114, K:E.114, K:H.117, L:E.52 FE.35: 4 residues within 4Å: Chain L: C.142, C.145, C.157, C.160 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.142, L:C.145, L:C.157, L:C.160 FE.36: 6 residues within 4Å: Chain K: E.52 Chain L: E.80, E.83, E.114, H.117 Ligands: FE.33 5 PLIP interactions: 3 interactions with chain L, 2 interactions with chain K Metal complexes: L:E.80, L:E.114, L:E.114, K:E.52, K:E.52 FE.37: 4 residues within 4Å: Chain M: C.142, C.145, C.157, C.160 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.142, M:C.145, M:C.157, M:C.160 FE.38: 6 residues within 4Å: Chain M: E.80, E.83, E.114 Chain N: Y.26, E.52 Ligands: FE.39 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:E.80, M:E.80 FE.39: 5 residues within 4Å: Chain M: E.80, E.83, E.114 Chain N: E.52 Ligands: FE.38 4 PLIP interactions: 3 interactions with chain M, 1 interactions with chain N Metal complexes: M:E.83, M:E.114, M:E.114, N:E.52 FE.40: 5 residues within 4Å: Chain M: E.19, E.52 Chain N: E.83, E.114 Ligands: FE.42 5 PLIP interactions: 3 interactions with chain M, 2 interactions with chain N Metal complexes: M:E.19, M:E.19, M:E.52, N:E.114, N:E.114 FE.41: 4 residues within 4Å: Chain N: C.142, C.145, C.157, C.160 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.142, N:C.145, N:C.157, N:C.160 FE.42: 5 residues within 4Å: Chain M: E.52 Chain N: E.80, E.114, H.117 Ligands: FE.40 5 PLIP interactions: 1 interactions with chain M, 4 interactions with chain N Metal complexes: M:E.52, N:E.80, N:E.80, N:E.114, N:H.117 FE.43: 4 residues within 4Å: Chain O: C.142, C.145, C.157, C.160 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.142, O:C.145, O:C.157, O:C.160 FE.44: 4 residues within 4Å: Chain O: E.83, E.114 Chain P: E.19, E.52 5 PLIP interactions: 3 interactions with chain O, 2 interactions with chain P Metal complexes: O:E.83, O:E.114, O:E.114, P:E.19, P:E.19 FE.45: 5 residues within 4Å: Chain O: E.80, H.117 Chain P: Y.26, I.48, E.52 2 PLIP interactions: 1 interactions with chain O, 1 interactions with chain P Metal complexes: O:E.80, P:Y.26 FE.46: 4 residues within 4Å: Chain P: C.142, C.145, C.157, C.160 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:C.142, P:C.145, P:C.157, P:C.160 FE.47: 6 residues within 4Å: Chain O: E.52 Chain P: E.80, E.83, E.114, H.117 Ligands: FE.48 4 PLIP interactions: 3 interactions with chain P, 1 interactions with chain O Metal complexes: P:E.80, P:E.114, P:E.114, O:E.52 FE.48: 5 residues within 4Å: Chain O: E.19, E.52 Chain P: E.83, E.114 Ligands: FE.47 5 PLIP interactions: 3 interactions with chain P, 2 interactions with chain O Metal complexes: P:E.83, P:E.83, P:E.114, O:E.19, O:E.19

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Song, W. et al., Structure of an oxygen-induced tubular nanocompartment in Pyrococcus furiosus. Elife (2025)

Release Date

2025-07-16

Peptides

Rubrerythrin: ABCDEFGHIJKLMNOP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

Rubrerythrin

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