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

Crystal structure of a YjeF family protein from Cryptococcus neoformans var. grubii serotype A in complex with AMPPNP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-octamer

Ligands

8 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 17 residues within 4Å: Chain A: N.178, K.216, G.217, P.218, D.220, G.251, R.254, G.256, G.257, Q.258, G.259, D.260, N.310, R.311 Chain D: P.30, K.34 Ligands: MG.2 24 PLIP interactions: 19 interactions with chain A, 5 interactions with chain D Hydrogen bonds: A:N.178, A:K.216, A:D.220, A:R.254, A:R.254, A:G.257, A:G.257, A:Q.258, A:G.259, A:D.260, A:N.310, A:R.311, D:P.30, D:K.34, D:K.34, D:K.34 Water bridges: A:G.250, A:R.311, A:S.314, A:S.314, D:K.34 Salt bridges: A:K.216 pi-Cation interactions: A:R.254, A:R.254 ANP.5: 17 residues within 4Å: Chain B: N.178, K.216, G.217, P.218, D.220, G.251, R.254, G.256, G.257, Q.258, G.259, D.260, N.310, R.311 Chain C: P.30, K.34 Ligands: MG.6 24 PLIP interactions: 19 interactions with chain B, 5 interactions with chain C Hydrogen bonds: B:N.178, B:K.216, B:D.220, B:R.254, B:R.254, B:G.257, B:G.257, B:Q.258, B:G.259, B:D.260, B:N.310, B:R.311, C:P.30, C:K.34, C:K.34, C:K.34 Water bridges: B:G.250, B:R.311, B:S.314, B:S.314, C:K.34 Salt bridges: B:K.216 pi-Cation interactions: B:R.254, B:R.254 ANP.9: 17 residues within 4Å: Chain A: P.30, K.34 Chain C: N.178, K.216, G.217, P.218, D.220, G.251, R.254, G.256, G.257, Q.258, G.259, D.260, N.310, R.311 Ligands: MG.10 24 PLIP interactions: 5 interactions with chain A, 19 interactions with chain C Hydrogen bonds: A:P.30, A:K.34, A:K.34, A:K.34, C:N.178, C:K.216, C:D.220, C:R.254, C:R.254, C:G.257, C:G.257, C:Q.258, C:G.259, C:D.260, C:N.310, C:R.311 Water bridges: A:K.34, C:G.250, C:R.311, C:S.314, C:S.314 Salt bridges: C:K.216 pi-Cation interactions: C:R.254, C:R.254 ANP.13: 17 residues within 4Å: Chain B: P.30, K.34 Chain D: N.178, K.216, G.217, P.218, D.220, G.251, R.254, G.256, G.257, Q.258, G.259, D.260, N.310, R.311 Ligands: MG.14 24 PLIP interactions: 19 interactions with chain D, 5 interactions with chain B Hydrogen bonds: D:N.178, D:K.216, D:D.220, D:R.254, D:R.254, D:G.257, D:G.257, D:Q.258, D:G.259, D:D.260, D:N.310, D:R.311, B:P.30, B:K.34, B:K.34, B:K.34 Water bridges: D:G.250, D:R.311, D:S.314, D:S.314, B:K.34 Salt bridges: D:K.216 pi-Cation interactions: D:R.254, D:R.254 ANP.17: 17 residues within 4Å: Chain E: N.178, K.216, G.217, P.218, D.220, G.251, R.254, G.256, G.257, Q.258, G.259, D.260, N.310, R.311 Chain H: P.30, K.34 Ligands: MG.18 24 PLIP interactions: 19 interactions with chain E, 5 interactions with chain H Hydrogen bonds: E:N.178, E:K.216, E:D.220, E:R.254, E:R.254, E:G.257, E:G.257, E:Q.258, E:G.259, E:D.260, E:N.310, E:R.311, H:P.30, H:K.34, H:K.34, H:K.34 Water bridges: E:G.250, E:R.311, E:S.314, E:S.314, H:K.34 Salt bridges: E:K.216 pi-Cation interactions: E:R.254, E:R.254 ANP.21: 17 residues within 4Å: Chain F: N.178, K.216, G.217, P.218, D.220, G.251, R.254, G.256, G.257, Q.258, G.259, D.260, N.310, R.311 Chain G: P.30, K.34 Ligands: MG.22 24 PLIP interactions: 19 interactions with chain F, 5 interactions with chain G Hydrogen bonds: F:N.178, F:K.216, F:D.220, F:R.254, F:R.254, F:G.257, F:G.257, F:Q.258, F:G.259, F:D.260, F:N.310, F:R.311, G:P.30, G:K.34, G:K.34, G:K.34 Water bridges: F:G.250, F:R.311, F:S.314, F:S.314, G:K.34 Salt bridges: F:K.216 pi-Cation interactions: F:R.254, F:R.254 ANP.25: 17 residues within 4Å: Chain E: P.30, K.34 Chain G: N.178, K.216, G.217, P.218, D.220, G.251, R.254, G.256, G.257, Q.258, G.259, D.260, N.310, R.311 Ligands: MG.26 24 PLIP interactions: 19 interactions with chain G, 5 interactions with chain E Hydrogen bonds: G:N.178, G:K.216, G:D.220, G:R.254, G:R.254, G:G.257, G:G.257, G:Q.258, G:G.259, G:D.260, G:N.310, G:R.311, E:P.30, E:K.34, E:K.34, E:K.34 Water bridges: G:G.250, G:R.311, G:S.314, G:S.314, E:K.34 Salt bridges: G:K.216 pi-Cation interactions: G:R.254, G:R.254 ANP.29: 17 residues within 4Å: Chain F: P.30, K.34 Chain H: N.178, K.216, G.217, P.218, D.220, G.251, R.254, G.256, G.257, Q.258, G.259, D.260, N.310, R.311 Ligands: MG.30 24 PLIP interactions: 19 interactions with chain H, 5 interactions with chain F Hydrogen bonds: H:N.178, H:K.216, H:D.220, H:R.254, H:R.254, H:G.257, H:G.257, H:Q.258, H:G.259, H:D.260, H:N.310, H:R.311, F:P.30, F:K.34, F:K.34, F:K.34 Water bridges: H:G.250, H:R.311, H:S.314, H:S.314, F:K.34 Salt bridges: H:K.216 pi-Cation interactions: H:R.254, H:R.254

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: K.216 Ligands: ANP.1 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain B: K.216 Ligands: ANP.5 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain C: K.216 Ligands: ANP.9 No protein-ligand interaction detected (PLIP) MG.14: 2 residues within 4Å: Chain D: K.216 Ligands: ANP.13 No protein-ligand interaction detected (PLIP) MG.18: 2 residues within 4Å: Chain E: K.216 Ligands: ANP.17 No protein-ligand interaction detected (PLIP) MG.22: 2 residues within 4Å: Chain F: K.216 Ligands: ANP.21 No protein-ligand interaction detected (PLIP) MG.26: 2 residues within 4Å: Chain G: K.216 Ligands: ANP.25 No protein-ligand interaction detected (PLIP) MG.30: 2 residues within 4Å: Chain H: K.216 Ligands: ANP.29 No protein-ligand interaction detected (PLIP)

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

PO4.3: 4 residues within 4Å: Chain A: R.99, H.127, S.130, C.131 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.130 Water bridges: A:H.127 Salt bridges: A:R.99, A:H.127 PO4.7: 4 residues within 4Å: Chain B: R.99, H.127, S.130, C.131 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.130 Water bridges: B:H.127 Salt bridges: B:R.99, B:H.127 PO4.11: 4 residues within 4Å: Chain C: R.99, H.127, S.130, C.131 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.130 Water bridges: C:H.127 Salt bridges: C:R.99, C:H.127 PO4.15: 4 residues within 4Å: Chain D: R.99, H.127, S.130, C.131 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.130 Water bridges: D:H.127 Salt bridges: D:R.99, D:H.127 PO4.19: 4 residues within 4Å: Chain E: R.99, H.127, S.130, C.131 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:S.130 Water bridges: E:H.127 Salt bridges: E:R.99, E:H.127 PO4.23: 4 residues within 4Å: Chain F: R.99, H.127, S.130, C.131 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:S.130 Water bridges: F:H.127 Salt bridges: F:R.99, F:H.127 PO4.27: 4 residues within 4Å: Chain G: R.99, H.127, S.130, C.131 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:S.130 Water bridges: G:H.127 Salt bridges: G:R.99, G:H.127 PO4.31: 4 residues within 4Å: Chain H: R.99, H.127, S.130, C.131 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:S.130 Water bridges: H:H.127 Salt bridges: H:R.99, H:H.127

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 5 residues within 4Å: Chain A: G.335, E.336 Chain C: K.320, K.321, S.324 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain C Water bridges: A:E.339, C:K.320, C:K.321, C:K.321, C:K.321 EDO.8: 5 residues within 4Å: Chain B: G.335, E.336 Chain D: K.320, K.321, S.324 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain D Water bridges: B:E.339, D:K.320, D:K.321, D:K.321, D:K.321 EDO.12: 5 residues within 4Å: Chain B: K.320, K.321, S.324 Chain C: G.335, E.336 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain B Water bridges: C:E.339, B:K.320, B:K.321, B:K.321, B:K.321 EDO.16: 5 residues within 4Å: Chain A: K.320, K.321, S.324 Chain D: G.335, E.336 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain D Water bridges: A:K.320, A:K.321, A:K.321, A:K.321, D:E.339 EDO.20: 5 residues within 4Å: Chain E: G.335, E.336 Chain G: K.320, K.321, S.324 5 PLIP interactions: 3 interactions with chain G, 2 interactions with chain E Water bridges: G:K.320, G:K.321, G:K.321, E:E.339, E:E.339 EDO.24: 5 residues within 4Å: Chain F: G.335, E.336 Chain H: K.320, K.321, S.324 5 PLIP interactions: 3 interactions with chain H, 2 interactions with chain F Water bridges: H:K.320, H:K.321, H:K.321, F:E.339, F:E.339 EDO.28: 5 residues within 4Å: Chain F: K.320, K.321, S.324 Chain G: G.335, E.336 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain G Water bridges: F:K.320, F:K.321, F:K.321, F:K.321, G:E.339 EDO.32: 5 residues within 4Å: Chain E: K.320, K.321, S.324 Chain H: G.335, E.336 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain H Water bridges: E:K.320, E:K.321, E:K.321, E:K.321, H:E.339

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 in complex with AMPPNP. 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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