SMTL ID : 7su8.1

DIHYDRONEOPTERIN ALDOLASE (DHNA) FROM YERSINIA PESTIS with alkylated Cys50 CO-CRYSTALLIZED with 7,8-dihydroneopterin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-octamer

Ligands

8 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.1: 1 residues within 4Å: Chain A: V.71 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.71 MPD.5: 6 residues within 4Å: Chain A: S.34, I.36 Chain F: S.34, I.36 Chain G: A.127, Q.128 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.36 Hydrogen bonds: A:S.34, A:S.34 MPD.6: 1 residues within 4Å: Chain B: V.71 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.71 MPD.10: 6 residues within 4Å: Chain B: S.34, I.36 Chain E: S.34, I.36 Chain H: A.127, Q.128 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.36 Hydrogen bonds: B:S.34, B:S.34 MPD.11: 1 residues within 4Å: Chain C: V.71 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.71 MPD.15: 6 residues within 4Å: Chain C: S.34, I.36 Chain F: A.127, Q.128 Chain H: S.34, I.36 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.36 Hydrogen bonds: C:S.34, C:S.34 MPD.16: 1 residues within 4Å: Chain D: V.71 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:V.71 MPD.20: 6 residues within 4Å: Chain D: S.34, I.36 Chain E: A.127, Q.128 Chain G: S.34, I.36 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:I.36 Hydrogen bonds: D:S.34, D:S.34

8 x NEN: 1-ETHYL-PYRROLIDINE-2,5-DIONE(Covalent)

NEN.2: 8 residues within 4Å: Chain A: A.65, D.69, D.70, N.72, D.73, C.74 Chain C: Y.42, L.95 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:L.95 Hydrogen bonds: A:N.72 NEN.7: 8 residues within 4Å: Chain B: A.65, D.69, D.70, N.72, D.73, C.74 Chain D: Y.42, L.95 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:N.72 Hydrophobic interactions: D:L.95 NEN.12: 8 residues within 4Å: Chain B: Y.42, L.95 Chain C: A.65, D.69, D.70, N.72, D.73, C.74 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:L.95 Hydrogen bonds: C:N.72 NEN.17: 8 residues within 4Å: Chain A: Y.42, L.95 Chain D: A.65, D.69, D.70, N.72, D.73, C.74 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:L.95 Hydrogen bonds: D:N.72 NEN.21: 8 residues within 4Å: Chain E: A.65, S.68, D.69, D.70, V.71, C.74 Chain H: V.41, L.95 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:D.69 NEN.23: 8 residues within 4Å: Chain F: A.65, S.68, D.69, D.70, V.71, C.74 Chain G: V.41, L.95 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:D.69 NEN.25: 8 residues within 4Å: Chain E: V.41, L.95 Chain G: A.65, S.68, D.69, D.70, V.71, C.74 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:D.69 NEN.27: 8 residues within 4Å: Chain F: V.41, L.95 Chain H: A.65, S.68, D.69, D.70, V.71, C.74 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:D.69

8 x PH2: 2-AMINO-6-HYDROXYMETHYL-7,8-DIHYDRO-3H-PTERIDIN-4-ONE(Non-covalent)

PH2.3: 11 residues within 4Å: Chain A: C.74, L.75, S.76, Y.77 Chain C: I.39, E.45, A.94, L.95, V.96, E.97, K.122 9 PLIP interactions: 3 interactions with chain C, 6 interactions with chain A Hydrogen bonds: C:I.39, C:V.96, A:L.75, A:Y.77 Salt bridges: C:E.97 Water bridges: A:L.75, A:Y.77, A:Y.77 pi-Stacking: A:Y.77 PH2.8: 11 residues within 4Å: Chain B: C.74, L.75, S.76, Y.77 Chain D: I.39, E.45, A.94, L.95, V.96, E.97, K.122 9 PLIP interactions: 3 interactions with chain D, 6 interactions with chain B Hydrogen bonds: D:I.39, D:V.96, B:L.75, B:Y.77 Salt bridges: D:E.97 Water bridges: B:L.75, B:Y.77, B:Y.77 pi-Stacking: B:Y.77 PH2.13: 11 residues within 4Å: Chain B: I.39, E.45, A.94, L.95, V.96, E.97, K.122 Chain C: C.74, L.75, S.76, Y.77 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain C Hydrogen bonds: B:I.39, B:V.96, C:L.75, C:Y.77 Salt bridges: B:E.97 Water bridges: C:L.75, C:Y.77, C:Y.77 pi-Stacking: C:Y.77 PH2.18: 11 residues within 4Å: Chain A: I.39, E.45, A.94, L.95, V.96, E.97, K.122 Chain D: C.74, L.75, S.76, Y.77 9 PLIP interactions: 6 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:L.75, D:Y.77, A:I.39, A:V.96 Water bridges: D:L.75, D:Y.77, D:Y.77 pi-Stacking: D:Y.77 Salt bridges: A:E.97 PH2.22: 9 residues within 4Å: Chain E: E.45, V.96, E.97, K.122, A.125 Chain G: C.74, L.75, S.76, Y.77 7 PLIP interactions: 4 interactions with chain E, 3 interactions with chain G Hydrogen bonds: E:V.96, E:K.122, E:A.125, G:L.75, G:Y.77 Salt bridges: E:E.97 pi-Cation interactions: G:Y.77 PH2.24: 9 residues within 4Å: Chain F: E.45, V.96, E.97, K.122, A.125 Chain H: C.74, L.75, S.76, Y.77 7 PLIP interactions: 3 interactions with chain H, 4 interactions with chain F Hydrogen bonds: H:L.75, H:Y.77, F:V.96, F:K.122, F:A.125 pi-Cation interactions: H:Y.77 Salt bridges: F:E.97 PH2.26: 9 residues within 4Å: Chain F: C.74, L.75, S.76, Y.77 Chain G: E.45, V.96, E.97, K.122, A.125 7 PLIP interactions: 4 interactions with chain G, 3 interactions with chain F Hydrogen bonds: G:V.96, G:K.122, G:A.125, F:L.75, F:Y.77 Salt bridges: G:E.97 pi-Cation interactions: F:Y.77 PH2.28: 9 residues within 4Å: Chain E: C.74, L.75, S.76, Y.77 Chain H: E.45, V.96, E.97, K.122, A.125 7 PLIP interactions: 4 interactions with chain H, 3 interactions with chain E Hydrogen bonds: H:V.96, H:K.122, H:A.125, E:L.75, E:Y.77 Salt bridges: H:E.97 pi-Cation interactions: E:Y.77

4 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.4: 7 residues within 4Å: Chain A: E.32, V.53, K.119, S.121, K.130, N.131 Chain D: E.31 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.32, A:K.119, A:K.119, A:S.121, A:N.131, A:N.131 TRS.9: 7 residues within 4Å: Chain B: E.32, V.53, K.119, S.121, K.130, N.131 Chain C: E.31 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.32, B:K.119, B:K.119, B:S.121, B:N.131, B:N.131 TRS.14: 7 residues within 4Å: Chain A: E.31 Chain C: E.32, V.53, K.119, S.121, K.130, N.131 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:E.32, C:K.119, C:K.119, C:S.121, C:N.131, C:N.131 TRS.19: 7 residues within 4Å: Chain B: E.31 Chain D: E.32, V.53, K.119, S.121, K.130, N.131 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:E.32, D:K.119, D:K.119, D:S.121, D:N.131, D:N.131

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bourne, C.R., DIHYDRONEOPTERIN ALDOLASE (DHNA) FROM YERSINIA PESTIS with alkylated Cys50 CO-CRYSTALLIZED with 7,8-dihydroneopterin. To Be Published

Release Date

2022-12-28

Peptides

7,8-dihydroneopterin aldolase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

C
B

D
B

E
A

F
A

G
A

H
A

7,8-dihydroneopterin aldolase

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