SMTL ID : 2e7d.1 (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-12-mer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: V.36, E.37, H.38, K.56 Chain E: K.56 Chain K: K.79 Ligand excluded by PLIP SO4.2: 5 residues within 4Å: Chain A: N.106 Chain C: T.12, D.13, L.14 Chain I: K.76 Ligand excluded by PLIP SO4.5: 4 residues within 4Å: Chain B: V.36, E.37, H.38, K.56 Ligand excluded by PLIP SO4.7: 6 residues within 4Å: Chain A: K.56 Chain C: V.36, E.37, H.38, K.56 Chain I: K.79 Ligand excluded by PLIP SO4.8: 5 residues within 4Å: Chain C: N.106 Chain E: T.12, D.13, L.14 Chain G: K.76 Ligand excluded by PLIP SO4.11: 4 residues within 4Å: Chain D: V.36, E.37, H.38, K.56 Ligand excluded by PLIP SO4.13: 6 residues within 4Å: Chain C: K.56 Chain E: V.36, E.37, H.38, K.56 Chain G: K.79 Ligand excluded by PLIP SO4.14: 5 residues within 4Å: Chain A: T.12, D.13, L.14 Chain E: N.106 Chain K: K.76 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain F: V.36, E.37, H.38, K.56 Ligand excluded by PLIP SO4.19: 6 residues within 4Å: Chain E: K.79 Chain G: V.36, E.37, H.38, K.56 Chain K: K.56 Ligand excluded by PLIP SO4.20: 5 residues within 4Å: Chain C: K.76 Chain G: N.106 Chain I: T.12, D.13, L.14 Ligand excluded by PLIP SO4.23: 4 residues within 4Å: Chain H: V.36, E.37, H.38, K.56 Ligand excluded by PLIP SO4.25: 6 residues within 4Å: Chain C: K.79 Chain G: K.56 Chain I: V.36, E.37, H.38, K.56 Ligand excluded by PLIP SO4.26: 5 residues within 4Å: Chain A: K.76 Chain I: N.106 Chain K: T.12, D.13, L.14 Ligand excluded by PLIP SO4.29: 4 residues within 4Å: Chain J: V.36, E.37, H.38, K.56 Ligand excluded by PLIP SO4.31: 6 residues within 4Å: Chain A: K.79 Chain I: K.56 Chain K: V.36, E.37, H.38, K.56 Ligand excluded by PLIP SO4.32: 5 residues within 4Å: Chain E: K.76 Chain G: T.12, D.13, L.14 Chain K: N.106 Ligand excluded by PLIP SO4.35: 4 residues within 4Å: Chain L: V.36, E.37, H.38, K.56 Ligand excluded by PLIP

6 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 ACT.21: 3 residues within 4Å: Chain G: K.93, A.94, V.95 5 PLIP interactions: 5 interactions with chain G Hydrophobic interactions: G:K.93 Hydrogen bonds: G:A.94, G:V.95, G:V.95 Salt bridges: G:K.93 ACT.27: 3 residues within 4Å: Chain I: K.93, A.94, V.95 5 PLIP interactions: 5 interactions with chain I Hydrophobic interactions: I:K.93 Hydrogen bonds: I:A.94, I:V.95, I:V.95 Salt bridges: I:K.93 ACT.33: 3 residues within 4Å: Chain K: K.93, A.94, V.95 5 PLIP interactions: 5 interactions with chain K Hydrophobic interactions: K:K.93 Hydrogen bonds: K:A.94, K:V.95, K:V.95 Salt bridges: K:K.93

12 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 GOL.22: 7 residues within 4Å: Chain G: D.58, W.61, K.62, D.63, L.64, V.71, R.83 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:D.63, G:D.63 GOL.24: 7 residues within 4Å: Chain H: D.58, W.61, K.62, D.63, L.64, R.83, L.85 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:D.63, H:L.64 GOL.28: 7 residues within 4Å: Chain I: D.58, W.61, K.62, D.63, L.64, V.71, R.83 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:D.63, I:D.63 GOL.30: 7 residues within 4Å: Chain J: D.58, W.61, K.62, D.63, L.64, R.83, L.85 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:D.63, J:L.64 GOL.34: 7 residues within 4Å: Chain K: D.58, W.61, K.62, D.63, L.64, V.71, R.83 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:D.63, K:D.63 GOL.36: 7 residues within 4Å: Chain L: D.58, W.61, K.62, D.63, L.64, R.83, L.85 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:D.63, L: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: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

I
A

J
B

K
A

L
B

Hypothetical protein IsdH

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