SMTL ID : 4ntm.1

QueD soaked with sepiapterin (selenomethionine substituted protein)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-hexamer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.16, H.31, H.33, E.110 Ligands: 2K8.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.16, A:H.31, A:H.33 ZN.3: 5 residues within 4Å: Chain B: H.16, H.31, H.33, E.110 Ligands: 2K8.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.16, B:H.31, B:H.33 ZN.5: 5 residues within 4Å: Chain C: H.16, H.31, H.33, E.110 Ligands: 2K8.6 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.16, C:H.31, C:H.33 ZN.7: 5 residues within 4Å: Chain D: H.16, H.31, H.33, E.110 Ligands: 2K8.8 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.16, D:H.31, D:H.33 ZN.9: 5 residues within 4Å: Chain E: H.16, H.31, H.33, E.110 Ligands: 2K8.10 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:H.16, E:H.31, E:H.33 ZN.11: 5 residues within 4Å: Chain F: H.16, H.31, H.33, E.110 Ligands: 2K8.12 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:H.16, F:H.31, F:H.33

6 x 2K8: (6R)-2-amino-4-oxo-3,4,5,6,7,8-hexahydropteridine-6-carboxylic acid(Non-covalent)

2K8.2: 16 residues within 4Å: Chain A: H.16, L.18, C.27, H.31, H.33, T.84, S.85, E.86, E.110 Chain C: H.71 Chain E: L.6, W.51, I.53, D.54, F.55 Ligands: ZN.1 13 PLIP interactions: 7 interactions with chain A, 5 interactions with chain E, 1 interactions with chain C Hydrogen bonds: A:S.85, A:E.110, E:I.53, E:F.55 Salt bridges: A:H.16, A:H.31, A:H.33, A:E.86, A:E.110, E:D.54, C:H.71 pi-Stacking: E:F.55 pi-Cation interactions: E:F.55 2K8.4: 16 residues within 4Å: Chain A: L.6, W.51, I.53, D.54, F.55 Chain B: H.16, L.18, C.27, H.31, H.33, T.84, S.85, E.86, E.110 Chain D: H.71 Ligands: ZN.3 12 PLIP interactions: 6 interactions with chain B, 5 interactions with chain A, 1 interactions with chain D Hydrogen bonds: B:S.85, B:E.110, A:I.53, A:F.55 Salt bridges: B:H.16, B:H.31, B:H.33, B:E.86, A:D.54, D:H.71 pi-Stacking: A:F.55 pi-Cation interactions: A:F.55 2K8.6: 16 residues within 4Å: Chain A: H.71 Chain C: H.16, L.18, C.27, H.31, H.33, T.84, S.85, E.86, E.110 Chain D: L.6, W.51, I.53, D.54, F.55 Ligands: ZN.5 11 PLIP interactions: 6 interactions with chain C, 1 interactions with chain A, 4 interactions with chain D Hydrogen bonds: C:S.85, C:E.110, D:I.53, D:F.55 Salt bridges: C:H.16, C:H.31, C:H.33, C:E.86, A:H.71 pi-Stacking: D:F.55 pi-Cation interactions: D:F.55 2K8.8: 16 residues within 4Å: Chain B: H.71 Chain D: H.16, L.18, C.27, H.31, H.33, T.84, S.85, E.86, E.110 Chain F: L.6, W.51, I.53, D.54, F.55 Ligands: ZN.7 13 PLIP interactions: 5 interactions with chain F, 7 interactions with chain D, 1 interactions with chain B Hydrogen bonds: F:I.53, F:D.54, F:F.55, D:S.85, D:S.85, D:E.110 pi-Stacking: F:F.55 pi-Cation interactions: F:F.55 Salt bridges: D:H.16, D:H.31, D:H.33, D:E.86, B:H.71 2K8.10: 16 residues within 4Å: Chain B: L.6, W.51, I.53, D.54, F.55 Chain E: H.16, L.18, C.27, H.31, H.33, T.84, S.85, E.86, E.110 Chain F: H.71 Ligands: ZN.9 12 PLIP interactions: 6 interactions with chain E, 1 interactions with chain F, 5 interactions with chain B Hydrogen bonds: E:S.85, E:E.110, B:I.53, B:D.54, B:F.55 Salt bridges: E:H.16, E:H.31, E:H.33, E:E.86, F:H.71 pi-Stacking: B:F.55 pi-Cation interactions: B:F.55 2K8.12: 15 residues within 4Å: Chain C: L.6, W.51, I.53, D.54, F.55 Chain E: H.71 Chain F: H.16, L.18, H.31, H.33, T.84, S.85, E.86, E.110 Ligands: ZN.11 11 PLIP interactions: 6 interactions with chain F, 1 interactions with chain E, 4 interactions with chain C Hydrogen bonds: F:S.85, F:E.110, C:I.53, C:F.55 Salt bridges: F:H.16, F:H.31, F:H.33, F:E.86, E:H.71 pi-Stacking: C:F.55 pi-Cation interactions: C:F.55

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miles, Z.D. et al., Biochemical and Structural Studies of 6-Carboxy-5,6,7,8-tetrahydropterin Synthase Reveal the Molecular Basis of Catalytic Promiscuity within the Tunnel-fold Superfamily. J.Biol.Chem. (2014)

Release Date

2014-07-16

Peptides

6-carboxy-5,6,7,8-tetrahydropterin synthase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

6-carboxy-5,6,7,8-tetrahydropterin synthase

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