SMTL ID : 6efw.2 (1 other biounit)

Crystal structure of a YjeF family protein from Cryptococcus neoformans var. grubii serotype A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-octamer

Ligands

8 x NA: SODIUM ION(Non-functional Binders)

NA.1: 3 residues within 4Å: Ligands: NA.3, NA.5, NA.7 4 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C, 1 interactions with chain A Water bridges: D:T.82, C:T.82, C:T.82, A:T.82 NA.3: 3 residues within 4Å: Ligands: NA.1, NA.5, NA.7 4 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A, 1 interactions with chain B Water bridges: D:T.82, D:T.82, A:T.82, B:T.82 NA.5: 3 residues within 4Å: Ligands: NA.1, NA.3, NA.7 6 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A, 3 interactions with chain B Water bridges: D:T.82, D:T.82, A:T.82, B:T.82, B:T.82, B:T.82 NA.7: 3 residues within 4Å: Ligands: NA.1, NA.3, NA.5 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C, 2 interactions with chain A Water bridges: D:T.82, C:T.82, A:T.82, A:T.82 NA.9: 3 residues within 4Å: Ligands: NA.11, NA.13, NA.15 6 PLIP interactions: 2 interactions with chain H, 1 interactions with chain E, 2 interactions with chain F, 1 interactions with chain G Water bridges: H:T.82, H:T.82, E:T.82, F:T.82, F:T.82, G:T.82 NA.11: 3 residues within 4Å: Ligands: NA.9, NA.13, NA.15 6 PLIP interactions: 1 interactions with chain H, 2 interactions with chain E, 2 interactions with chain F, 1 interactions with chain G Water bridges: H:T.82, E:T.82, E:T.82, F:T.82, F:T.82, G:T.82 NA.13: 3 residues within 4Å: Ligands: NA.9, NA.11, NA.15 4 PLIP interactions: 2 interactions with chain H, 1 interactions with chain F, 1 interactions with chain G Water bridges: H:T.82, H:T.82, F:T.82, G:T.82 NA.15: 3 residues within 4Å: Ligands: NA.9, NA.11, NA.13 4 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F, 2 interactions with chain G Water bridges: E:T.82, F:T.82, G:T.82, G:T.82

8 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 5 residues within 4Å: Chain A: R.99, I.102, H.127, S.130, C.131 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.130, A:S.130 Salt bridges: A:H.127 PO4.4: 5 residues within 4Å: Chain B: R.99, I.102, H.127, S.130, C.131 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.130, B:S.130 Salt bridges: B:H.127 PO4.6: 5 residues within 4Å: Chain C: R.99, I.102, H.127, S.130, C.131 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.130, C:S.130 Salt bridges: C:H.127 PO4.8: 5 residues within 4Å: Chain D: R.99, I.102, H.127, S.130, C.131 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.130, D:S.130 Salt bridges: D:H.127 PO4.10: 5 residues within 4Å: Chain E: R.99, I.102, H.127, S.130, C.131 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:S.130, E:S.130 Salt bridges: E:H.127 PO4.12: 5 residues within 4Å: Chain F: R.99, I.102, H.127, S.130, C.131 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:S.130, F:S.130 Salt bridges: F:H.127 PO4.14: 5 residues within 4Å: Chain G: R.99, I.102, H.127, S.130, C.131 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:S.130, G:S.130 Salt bridges: G:H.127 PO4.16: 5 residues within 4Å: Chain H: R.99, I.102, H.127, S.130, C.131 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:S.130, H:S.130 Salt bridges: H:H.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abendroth, J. et al., Crystal structure of a YjeF family protein from Cryptococcus neoformans var. grubii serotype A. TO BE PUBLISHED

Release Date

2018-09-05

Peptides

ATP-dependent (S)-NAD(P)H-hydrate dehydratase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

ATP-dependent (S)-NAD(P)H-hydrate dehydratase

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