SMTL ID : 3dnc.1

Carboxysome shell protein, CcmK2 C-terminal deletion mutant, with a closer spacing between hexamers

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-hexamer

Ligands

12 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 3 residues within 4Å: Chain A: E.62, R.66 Ligands: GOL.3 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.66 SO4.2: 4 residues within 4Å: Chain A: R.11, S.39, R.41 Chain E: R.11 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:S.39 Salt bridges: A:R.11, A:R.41, E:R.11 SO4.4: 3 residues within 4Å: Chain B: E.62, R.66 Ligands: GOL.6 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.66 SO4.5: 4 residues within 4Å: Chain B: R.11, S.39, R.41 Chain F: R.11 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain F Hydrogen bonds: B:S.39 Salt bridges: B:R.11, B:R.41, F:R.11 SO4.7: 3 residues within 4Å: Chain C: E.62, R.66 Ligands: GOL.9 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.66 SO4.8: 4 residues within 4Å: Chain C: R.11, S.39, R.41 Chain D: R.11 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.39 Salt bridges: C:R.11, C:R.41, D:R.11 SO4.10: 3 residues within 4Å: Chain D: E.62, R.66 Ligands: GOL.12 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.66 SO4.11: 4 residues within 4Å: Chain B: R.11 Chain D: R.11, S.39, R.41 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:S.39 Salt bridges: D:R.11, D:R.41, B:R.11 SO4.13: 3 residues within 4Å: Chain E: E.62, R.66 Ligands: GOL.15 1 PLIP interactions: 1 interactions with chain E Salt bridges: E:R.66 SO4.14: 4 residues within 4Å: Chain C: R.11 Chain E: R.11, S.39, R.41 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:S.39 Salt bridges: E:R.11, E:R.41, C:R.11 SO4.16: 3 residues within 4Å: Chain F: E.62, R.66 Ligands: GOL.18 1 PLIP interactions: 1 interactions with chain F Salt bridges: F:R.66 SO4.17: 4 residues within 4Å: Chain A: R.11 Chain F: R.11, S.39, R.41 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:S.39 Salt bridges: F:R.11, F:R.41, A:R.11

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: S.22, A.59, E.62, A.63, R.66 Ligands: SO4.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.66, A:R.66 GOL.6: 6 residues within 4Å: Chain B: S.22, A.59, E.62, A.63, R.66 Ligands: SO4.4 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.66, B:R.66 GOL.9: 6 residues within 4Å: Chain C: S.22, A.59, E.62, A.63, R.66 Ligands: SO4.7 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.66, C:R.66 GOL.12: 6 residues within 4Å: Chain D: S.22, A.59, E.62, A.63, R.66 Ligands: SO4.10 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.66, D:R.66 GOL.15: 6 residues within 4Å: Chain E: S.22, A.59, E.62, A.63, R.66 Ligands: SO4.13 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.66, E:R.66 GOL.18: 6 residues within 4Å: Chain F: S.22, A.59, E.62, A.63, R.66 Ligands: SO4.16 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:R.66, F:R.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tanaka, S. et al., Insights from multiple structures of the shell proteins from the beta-carboxysome. Protein Sci. (2009)

Release Date

2009-01-20

Peptides

Carbon dioxide-concentrating mechanism protein ccmK homolog 2: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Carbon dioxide-concentrating mechanism protein ccmK homolog 2

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