SMTL ID : 2nm3.1

Crystal structure of dihydroneopterin aldolase from S. aureus in complex with (1S,2S)-monapterin at 1.68 angstrom resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

homo-octamer

Ligands

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

ACT.1: 6 residues within 4Å: Chain A: T.34, L.35, K.36, E.93, K.95, V.117 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:T.34, A:K.36, A:K.95 Salt bridges: A:K.95 Water bridges: D:Q.2 ACT.3: 6 residues within 4Å: Chain B: T.34, L.35, K.36, E.93, K.95, V.117 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:T.34, B:K.36, B:K.95 Salt bridges: B:K.95 Water bridges: C:Q.2 ACT.5: 6 residues within 4Å: Chain C: T.34, L.35, K.36, E.93, K.95, V.117 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain C Water bridges: A:Q.2 Hydrogen bonds: C:T.34, C:K.36, C:K.95 Salt bridges: C:K.95 ACT.7: 6 residues within 4Å: Chain D: T.34, L.35, K.36, E.93, K.95, V.117 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain D Water bridges: B:Q.2 Hydrogen bonds: D:T.34, D:K.36, D:K.95 Salt bridges: D:K.95 ACT.9: 6 residues within 4Å: Chain E: T.34, L.35, K.36, E.93, K.95, V.117 6 PLIP interactions: 1 interactions with chain H, 5 interactions with chain E Water bridges: H:Q.2 Hydrogen bonds: E:T.34, E:K.36, E:E.93, E:K.95 Salt bridges: E:K.95 ACT.11: 6 residues within 4Å: Chain F: T.34, L.35, K.36, E.93, K.95, V.117 6 PLIP interactions: 5 interactions with chain F, 1 interactions with chain G Hydrogen bonds: F:T.34, F:K.36, F:E.93, F:K.95 Salt bridges: F:K.95 Water bridges: G:Q.2 ACT.13: 6 residues within 4Å: Chain G: T.34, L.35, K.36, E.93, K.95, V.117 6 PLIP interactions: 5 interactions with chain G, 1 interactions with chain E Hydrogen bonds: G:T.34, G:K.36, G:E.93, G:K.95 Salt bridges: G:K.95 Water bridges: E:Q.2 ACT.15: 6 residues within 4Å: Chain H: T.34, L.35, K.36, E.93, K.95, V.117 6 PLIP interactions: 5 interactions with chain H, 1 interactions with chain F Hydrogen bonds: H:T.34, H:K.36, H:E.93, H:K.95 Salt bridges: H:K.95 Water bridges: F:Q.2

8 x MPU: D-MONAPTERIN(Non-covalent)

MPU.2: 15 residues within 4Å: Chain A: G.17, A.18, E.22, L.72, L.73, E.74, K.100, P.103, P.104 Chain D: I.5, T.51, V.52, H.53, Y.54, G.55 14 PLIP interactions: 5 interactions with chain A, 9 interactions with chain D Hydrogen bonds: A:A.18, A:N.71, A:L.73, A:K.100, D:T.51, D:V.52, D:Y.54, D:Y.54, D:G.55 Salt bridges: A:E.74 Water bridges: D:H.53 pi-Stacking: D:H.53, D:Y.54, D:Y.54 MPU.4: 15 residues within 4Å: Chain B: G.17, A.18, E.22, L.72, L.73, E.74, K.100, P.103, P.104 Chain C: I.5, T.51, V.52, H.53, Y.54, G.55 14 PLIP interactions: 5 interactions with chain B, 9 interactions with chain C Hydrogen bonds: B:A.18, B:N.71, B:L.73, B:K.100, C:T.51, C:V.52, C:Y.54, C:Y.54, C:G.55 Salt bridges: B:E.74 Water bridges: C:H.53 pi-Stacking: C:H.53, C:Y.54, C:Y.54 MPU.6: 15 residues within 4Å: Chain A: I.5, T.51, V.52, H.53, Y.54, G.55 Chain C: G.17, A.18, E.22, L.72, L.73, E.74, K.100, P.103, P.104 14 PLIP interactions: 5 interactions with chain C, 9 interactions with chain A Hydrogen bonds: C:A.18, C:N.71, C:L.73, C:K.100, A:T.51, A:V.52, A:Y.54, A:Y.54, A:G.55 Salt bridges: C:E.74 Water bridges: A:H.53 pi-Stacking: A:H.53, A:Y.54, A:Y.54 MPU.8: 15 residues within 4Å: Chain B: I.5, T.51, V.52, H.53, Y.54, G.55 Chain D: G.17, A.18, E.22, L.72, L.73, E.74, K.100, P.103, P.104 14 PLIP interactions: 9 interactions with chain B, 5 interactions with chain D Hydrogen bonds: B:T.51, B:V.52, B:Y.54, B:Y.54, B:G.55, D:A.18, D:N.71, D:L.73, D:K.100 Water bridges: B:H.53 pi-Stacking: B:H.53, B:Y.54, B:Y.54 Salt bridges: D:E.74 MPU.10: 15 residues within 4Å: Chain E: G.17, A.18, E.22, L.72, L.73, E.74, K.100, P.103, P.104 Chain H: I.5, T.51, V.52, H.53, Y.54, G.55 14 PLIP interactions: 5 interactions with chain E, 9 interactions with chain H Hydrogen bonds: E:A.18, E:N.71, E:L.73, E:K.100, H:V.52, H:Y.54, H:G.55 Salt bridges: E:E.74 Water bridges: H:H.53, H:Y.54, H:Y.54 pi-Stacking: H:H.53, H:Y.54, H:Y.54 MPU.12: 15 residues within 4Å: Chain F: G.17, A.18, E.22, L.72, L.73, E.74, K.100, P.103, P.104 Chain G: I.5, T.51, V.52, H.53, Y.54, G.55 14 PLIP interactions: 9 interactions with chain G, 5 interactions with chain F Hydrogen bonds: G:V.52, G:Y.54, G:G.55, F:A.18, F:N.71, F:L.73, F:K.100 Water bridges: G:H.53, G:Y.54, G:Y.54 pi-Stacking: G:H.53, G:Y.54, G:Y.54 Salt bridges: F:E.74 MPU.14: 15 residues within 4Å: Chain E: I.5, T.51, V.52, H.53, Y.54, G.55 Chain G: G.17, A.18, E.22, L.72, L.73, E.74, K.100, P.103, P.104 14 PLIP interactions: 9 interactions with chain E, 5 interactions with chain G Hydrogen bonds: E:V.52, E:Y.54, E:G.55, G:A.18, G:N.71, G:L.73, G:K.100 Water bridges: E:H.53, E:Y.54, E:Y.54 pi-Stacking: E:H.53, E:Y.54, E:Y.54 Salt bridges: G:E.74 MPU.16: 15 residues within 4Å: Chain F: I.5, T.51, V.52, H.53, Y.54, G.55 Chain H: G.17, A.18, E.22, L.72, L.73, E.74, K.100, P.103, P.104 14 PLIP interactions: 5 interactions with chain H, 9 interactions with chain F Hydrogen bonds: H:A.18, H:N.71, H:L.73, H:K.100, F:V.52, F:Y.54, F:G.55 Salt bridges: H:E.74 Water bridges: F:H.53, F:Y.54, F:Y.54 pi-Stacking: F:H.53, F:Y.54, F:Y.54

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Blaszczyk, J. et al., Structural basis for the aldolase and epimerase activities of Staphylococcus aureus dihydroneopterin aldolase. J.Mol.Biol. (2007)

Release Date

2007-09-04

Peptides

Dihydroneopterin aldolase: 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

Dihydroneopterin aldolase

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