SMTL ID : 5f3m.1

Crystal structure of dihydroneopterin aldolase from Bacillus anthracis complexed with L-neopterin at 1.5 Angstroms resolution .

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-octamer

Ligands

8 x NEU: L-NEOPTERIN(Non-covalent)

NEU.1: 17 residues within 4Å: Chain A: G.19, V.20, F.21, E.24, K.73, L.74, V.75, E.76, K.102, P.105, P.106 Chain E: I.7, L.50, S.53, V.54, N.55, Y.56 11 PLIP interactions: 6 interactions with chain E, 5 interactions with chain A Hydrogen bonds: E:S.53, E:V.54, E:Y.56, E:Y.56, A:V.20, A:V.75, A:K.102, A:K.102 pi-Stacking: E:Y.56, E:Y.56 Salt bridges: A:E.76 NEU.6: 17 residues within 4Å: Chain B: G.19, V.20, F.21, E.24, L.74, V.75, E.76, K.102, P.105, P.106, I.107 Chain H: I.7, L.50, S.53, V.54, N.55, Y.56 13 PLIP interactions: 5 interactions with chain B, 8 interactions with chain H Hydrogen bonds: B:V.20, B:V.75, B:K.102, B:K.102, H:S.53, H:V.54, H:Y.56, H:Y.56 Salt bridges: B:E.76 Water bridges: H:N.55, H:G.57 pi-Stacking: H:Y.56, H:Y.56 NEU.12: 17 residues within 4Å: Chain C: G.19, V.20, F.21, E.24, K.73, L.74, V.75, E.76, K.102, P.105, P.106 Chain G: I.7, L.50, S.53, V.54, N.55, Y.56 11 PLIP interactions: 6 interactions with chain G, 5 interactions with chain C Hydrogen bonds: G:S.53, G:V.54, G:Y.56, G:Y.56, C:V.20, C:V.75, C:K.102, C:K.102 pi-Stacking: G:Y.56, G:Y.56 Salt bridges: C:E.76 NEU.17: 17 residues within 4Å: Chain D: G.19, V.20, F.21, E.24, L.74, V.75, E.76, K.102, P.105, P.106, I.107 Chain F: I.7, L.50, S.53, V.54, N.55, Y.56 13 PLIP interactions: 8 interactions with chain F, 5 interactions with chain D Hydrogen bonds: F:S.53, F:V.54, F:Y.56, F:Y.56, D:V.20, D:V.75, D:K.102, D:K.102 Water bridges: F:N.55, F:G.57 pi-Stacking: F:Y.56, F:Y.56 Salt bridges: D:E.76 NEU.23: 17 residues within 4Å: Chain C: I.7, L.50, S.53, V.54, N.55, Y.56 Chain E: G.19, V.20, F.21, E.24, K.73, L.74, V.75, E.76, K.102, P.105, P.106 11 PLIP interactions: 6 interactions with chain C, 5 interactions with chain E Hydrogen bonds: C:S.53, C:V.54, C:Y.56, C:Y.56, E:V.20, E:V.75, E:K.102, E:K.102 pi-Stacking: C:Y.56, C:Y.56 Salt bridges: E:E.76 NEU.28: 17 residues within 4Å: Chain B: I.7, L.50, S.53, V.54, N.55, Y.56 Chain F: G.19, V.20, F.21, E.24, L.74, V.75, E.76, K.102, P.105, P.106, I.107 13 PLIP interactions: 8 interactions with chain B, 5 interactions with chain F Hydrogen bonds: B:S.53, B:V.54, B:Y.56, B:Y.56, F:V.20, F:V.75, F:K.102, F:K.102 Water bridges: B:N.55, B:G.57 pi-Stacking: B:Y.56, B:Y.56 Salt bridges: F:E.76 NEU.34: 17 residues within 4Å: Chain A: I.7, L.50, S.53, V.54, N.55, Y.56 Chain G: G.19, V.20, F.21, E.24, K.73, L.74, V.75, E.76, K.102, P.105, P.106 11 PLIP interactions: 5 interactions with chain G, 6 interactions with chain A Hydrogen bonds: G:V.20, G:V.75, G:K.102, G:K.102, A:S.53, A:V.54, A:Y.56, A:Y.56 Salt bridges: G:E.76 pi-Stacking: A:Y.56, A:Y.56 NEU.39: 17 residues within 4Å: Chain D: I.7, L.50, S.53, V.54, N.55, Y.56 Chain H: G.19, V.20, F.21, E.24, L.74, V.75, E.76, K.102, P.105, P.106, I.107 13 PLIP interactions: 5 interactions with chain H, 8 interactions with chain D Hydrogen bonds: H:V.20, H:V.75, H:K.102, H:K.102, D:S.53, D:V.54, D:Y.56, D:Y.56 Salt bridges: H:E.76 Water bridges: D:N.55, D:G.57 pi-Stacking: D:Y.56, D:Y.56

8 x NI: NICKEL (II) ION(Non-covalent)

NI.2: 2 residues within 4Å: Chain A: D.49, H.52 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.52, H2O.1, H2O.4 NI.7: 1 residues within 4Å: Chain B: H.52 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.52, H2O.8, H2O.8, H2O.8 NI.13: 2 residues within 4Å: Chain C: D.49, H.52 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.52, H2O.10, H2O.13 NI.18: 1 residues within 4Å: Chain D: H.52 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:H.52, H2O.17, H2O.17, H2O.17 NI.24: 2 residues within 4Å: Chain E: D.49, H.52 3 PLIP interactions: 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:H.52, H2O.19, H2O.22 NI.29: 1 residues within 4Å: Chain F: H.52 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:H.52, H2O.26, H2O.26, H2O.26 NI.35: 2 residues within 4Å: Chain G: D.49, H.52 3 PLIP interactions: 1 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:H.52, H2O.28, H2O.31 NI.40: 1 residues within 4Å: Chain H: H.52 4 PLIP interactions: 1 interactions with chain H, 3 Ligand-Water interactions Metal complexes: H:H.52, H2O.35, H2O.35, H2O.35

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

EDO.3: 4 residues within 4Å: Chain A: N.25, T.71, Y.72, K.73 Ligand excluded by PLIP EDO.4: 4 residues within 4Å: Chain A: K.99, E.117 Chain E: Y.8, H.10 Ligand excluded by PLIP EDO.5: 8 residues within 4Å: Chain A: A.44, G.45, E.46, S.47, D.48 Chain G: Y.72, S.77, N.81 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain B: Y.17, E.68, D.69, R.70, T.71 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain B: Q.29, D.104, P.105, P.106 Chain G: Q.29 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain C: N.25, T.71, Y.72, K.73 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain C: K.99, E.117 Chain G: Y.8, H.10 Ligand excluded by PLIP EDO.16: 8 residues within 4Å: Chain C: A.44, G.45, E.46, S.47, D.48 Chain E: Y.72, S.77, N.81 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain D: Y.17, E.68, D.69, R.70, T.71 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain D: Q.29, D.104, P.105, P.106 Chain E: Q.29 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain E: N.25, T.71, Y.72, K.73 Ligand excluded by PLIP EDO.26: 4 residues within 4Å: Chain C: Y.8, H.10 Chain E: K.99, E.117 Ligand excluded by PLIP EDO.27: 8 residues within 4Å: Chain A: Y.72, S.77, N.81 Chain E: A.44, G.45, E.46, S.47, D.48 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain F: Y.17, E.68, D.69, R.70, T.71 Ligand excluded by PLIP EDO.33: 5 residues within 4Å: Chain A: Q.29 Chain F: Q.29, D.104, P.105, P.106 Ligand excluded by PLIP EDO.36: 4 residues within 4Å: Chain G: N.25, T.71, Y.72, K.73 Ligand excluded by PLIP EDO.37: 4 residues within 4Å: Chain A: Y.8, H.10 Chain G: K.99, E.117 Ligand excluded by PLIP EDO.38: 8 residues within 4Å: Chain C: Y.72, S.77, N.81 Chain G: A.44, G.45, E.46, S.47, D.48 Ligand excluded by PLIP EDO.41: 5 residues within 4Å: Chain H: Y.17, E.68, D.69, R.70, T.71 Ligand excluded by PLIP EDO.44: 5 residues within 4Å: Chain C: Q.29 Chain H: Q.29, D.104, P.105, P.106 Ligand excluded by PLIP

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.9: 3 residues within 4Å: Chain B: Y.90, E.91, S.92 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain D: Y.90, E.91, S.92 Ligand excluded by PLIP CL.31: 3 residues within 4Å: Chain F: Y.90, E.91, S.92 Ligand excluded by PLIP CL.42: 3 residues within 4Å: Chain H: Y.90, E.91, S.92 Ligand excluded by PLIP

4 x FMT: FORMIC ACID(Non-functional Binders)

FMT.10: 3 residues within 4Å: Chain B: K.99, E.117 Chain H: Y.8 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain H Hydrogen bonds: B:E.117, H:Y.8 FMT.21: 3 residues within 4Å: Chain D: K.99, E.117 Chain F: Y.8 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain F Hydrogen bonds: D:E.117, F:Y.8 FMT.32: 3 residues within 4Å: Chain B: Y.8 Chain F: K.99, E.117 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain F Hydrogen bonds: B:Y.8, F:E.117 FMT.43: 3 residues within 4Å: Chain D: Y.8 Chain H: K.99, E.117 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain D Hydrogen bonds: H:E.117, D:Y.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maltseva, N. et al., Crystal structure of dihydroneopterin aldolase from Bacillus anthracis complexed with L-neopterin at 1.5 Angstroms resolution . To Be Published

Release Date

2015-12-23

Peptides

7,8-dihydroneopterin aldolase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

7,8-dihydroneopterin aldolase

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