SMTL ID : 2e7d.2 (1 other biounit)

Crystal structure of a NEAT domain from Staphylococcus aureus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: V.36, E.37, H.38, K.56 Chain E: K.56 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:V.36, A:H.38 Salt bridges: A:H.38, A:K.56, E:K.56 SO4.2: 4 residues within 4Å: Chain A: N.106 Chain C: T.12, D.13, L.14 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:T.12, C:D.13, C:L.14, A:N.106 SO4.5: 4 residues within 4Å: Chain B: V.36, E.37, H.38, K.56 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.36, B:H.38 Salt bridges: B:H.38, B:K.56 SO4.7: 5 residues within 4Å: Chain A: K.56 Chain C: V.36, E.37, H.38, K.56 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:V.36, C:H.38 Salt bridges: C:H.38, C:K.56, A:K.56 SO4.8: 4 residues within 4Å: Chain C: N.106 Chain E: T.12, D.13, L.14 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:T.12, E:D.13, E:L.14, C:N.106 SO4.11: 4 residues within 4Å: Chain D: V.36, E.37, H.38, K.56 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:V.36, D:H.38 Salt bridges: D:H.38, D:K.56 SO4.13: 5 residues within 4Å: Chain C: K.56 Chain E: V.36, E.37, H.38, K.56 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:V.36, E:H.38 Salt bridges: E:H.38, E:K.56, C:K.56 SO4.14: 4 residues within 4Å: Chain A: T.12, D.13, L.14 Chain E: N.106 4 PLIP interactions: 1 interactions with chain E, 3 interactions with chain A Hydrogen bonds: E:N.106, A:T.12, A:D.13, A:L.14 SO4.17: 4 residues within 4Å: Chain F: V.36, E.37, H.38, K.56 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:V.36, F:H.38 Salt bridges: F:H.38, F:K.56

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 3 residues within 4Å: Chain A: K.93, A.94, V.95 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.93 Hydrogen bonds: A:A.94, A:V.95, A:V.95 Salt bridges: A:K.93 ACT.9: 3 residues within 4Å: Chain C: K.93, A.94, V.95 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:K.93 Hydrogen bonds: C:A.94, C:V.95, C:V.95 Salt bridges: C:K.93 ACT.15: 3 residues within 4Å: Chain E: K.93, A.94, V.95 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:K.93 Hydrogen bonds: E:A.94, E:V.95, E:V.95 Salt bridges: E:K.93

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: D.58, W.61, K.62, D.63, L.64, V.71, R.83 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.63 GOL.6: 7 residues within 4Å: Chain B: D.58, W.61, K.62, D.63, L.64, R.83, L.85 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.63, B:D.63, B:L.64 GOL.10: 7 residues within 4Å: Chain C: D.58, W.61, K.62, D.63, L.64, V.71, R.83 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.63 GOL.12: 7 residues within 4Å: Chain D: D.58, W.61, K.62, D.63, L.64, R.83, L.85 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.63, D:D.63, D:L.64 GOL.16: 7 residues within 4Å: Chain E: D.58, W.61, K.62, D.63, L.64, V.71, R.83 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:D.63 GOL.18: 7 residues within 4Å: Chain F: D.58, W.61, K.62, D.63, L.64, R.83, L.85 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:D.63, F:D.63, F:L.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Watanabe, M. et al., Structural basis for multimeric heme complexation through a specific protein-heme interaction: the case of the third neat domain of IsdH from Staphylococcus aureus. J.Biol.Chem. (2008)

Release Date

2008-01-22

Peptides

Hypothetical protein IsdH: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Hypothetical protein IsdH

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