SMTL ID : 3vua.7 (6 other biounits)

Apo IsdH-NEAT3 in space group P3121 at a resolution of 1.85 A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-hexamer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: T.7, D.8, L.9 Chain C: N.101 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:D.8, A:L.9, C:N.101 SO4.2: 4 residues within 4Å: Chain A: V.31, E.32, H.33, K.51 7 PLIP interactions: 2 interactions with chain C, 5 interactions with chain A Water bridges: C:K.51, A:K.51, A:K.51 Salt bridges: C:K.51, A:H.33, A:K.51 Hydrogen bonds: A:H.33 SO4.8: 5 residues within 4Å: Chain C: V.31, E.32, H.33, K.51 Chain E: K.51 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain E Hydrogen bonds: C:H.33 Salt bridges: C:H.33, C:K.51, E:K.51 Water bridges: E:K.51, E:K.51 SO4.9: 3 residues within 4Å: Chain C: K.71, R.78 Ligands: GOL.6 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:K.71, C:R.78 SO4.13: 5 residues within 4Å: Chain A: K.51 Chain E: V.31, E.32, H.33, K.51 10 PLIP interactions: 6 interactions with chain E, 4 interactions with chain A Hydrogen bonds: E:V.31, E:H.33 Water bridges: E:K.51, E:K.51, A:K.51, A:K.51, A:K.51 Salt bridges: E:H.33, E:K.51, A:K.51 SO4.14: 4 residues within 4Å: Chain F: V.31, E.32, H.33, K.51 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:H.33, F:H.33 Water bridges: F:H.33, F:H.33, F:K.51 Salt bridges: F:H.33, F:K.51

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

ACT.3: 1 residues within 4Å: Chain A: K.71 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.71 ACT.10: 7 residues within 4Å: Chain C: K.49, S.70, K.71, D.72, S.77, R.78, T.79 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:D.72 Hydrogen bonds: C:S.77, C:T.79, C:T.79 Salt bridges: C:K.49

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 9 residues within 4Å: Chain B: T.50, D.53, W.56, K.57, D.58, L.59, V.66, R.78, L.80 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:D.53, B:D.58, B:L.59, B:R.78 Water bridges: B:D.53, B:D.53, B:V.66, B:T.68 GOL.5: 5 residues within 4Å: Chain C: E.11, D.116 Chain E: V.99, Y.104 Chain F: Y.108 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain E, 2 interactions with chain F Hydrogen bonds: C:D.116, F:Y.108, F:Y.108 Water bridges: E:Y.55 GOL.6: 10 residues within 4Å: Chain C: D.53, W.56, K.57, D.58, L.59, R.65, V.66, R.78, L.80 Ligands: SO4.9 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.53, C:L.59 Water bridges: C:V.66, C:R.78 GOL.7: 3 residues within 4Å: Chain C: D.87, K.88, A.89 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.87, C:K.88, C:A.89, C:V.90 GOL.11: 9 residues within 4Å: Chain D: T.50, D.53, W.56, K.57, D.58, L.59, V.66, R.78, L.80 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:D.53, D:D.58, D:L.59 Water bridges: D:D.53, D:W.56, D:V.66, D:T.68 GOL.12: 8 residues within 4Å: Chain A: Y.55, V.99, I.102, Y.104 Chain B: V.26, Y.108 Chain E: Q.10, E.11 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain E, 2 interactions with chain A Hydrogen bonds: B:Y.108, E:Q.10, A:Y.55, A:Y.55

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vu, N.T. et al., Structure of heme transport protein IsdH-NEAT3 from S. aureus in complex with Indium-porphyrin. To be Published

Release Date

2013-06-26

Peptides

Iron-regulated surface determinant protein H: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Iron-regulated surface determinant protein H

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