SMTL ID : 4cwx.1

ALPHA-KETOGLUTARATE-DEPENDENT DIOXYGENASE COMPLEX1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 20 residues within 4Å: Chain A: W.141, R.146, C.147, V.148, G.149, S.189, M.302, F.316, S.317, G.318, W.319, M.321, E.324, V.381, W.410, F.436, Y.438 Ligands: H4B.2, HW0.3, ACT.4 21 PLIP interactions: 21 interactions with chain A, Hydrophobic interactions: A:W.141, A:W.141, A:R.146, A:F.316, A:F.316, A:F.316, A:F.316, A:W.319, A:E.324, A:V.381, A:W.410, A:F.436, A:F.436, A:F.436 Hydrogen bonds: A:Y.438 Water bridges: A:E.324, A:E.324, A:R.328, A:Y.438 pi-Stacking: A:W.141 Metal complexes: A:C.147 HEM.6: 19 residues within 4Å: Chain B: W.141, R.146, C.147, V.148, G.149, S.189, M.302, F.316, S.317, G.318, W.319, M.321, E.324, V.381, W.410, F.436, Y.438 Ligands: H4B.7, HW0.8 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:W.141, B:W.141, B:W.141, B:F.316, B:F.316, B:F.316, B:F.316, B:W.319, B:E.324, B:V.381, B:W.410, B:F.436, B:F.436, B:F.436 Water bridges: B:E.324, B:R.328, B:Y.438 pi-Stacking: B:W.141 Metal complexes: B:C.147

2 x H4B: 5,6,7,8-TETRAHYDROBIOPTERIN(Non-covalent)

H4B.2: 12 residues within 4Å: Chain A: S.65, V.67, R.328, A.409, W.410 Chain B: W.408, F.423, H.424, Q.425, E.426 Ligands: HEM.1, HW0.3 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.328, A:A.409, A:W.410 Water bridges: A:R.328, A:R.328, A:R.328, B:H.424 pi-Stacking: A:W.410, A:W.410 pi-Cation interactions: A:W.410, A:W.410 Hydrophobic interactions: B:E.426 H4B.7: 13 residues within 4Å: Chain A: W.37, W.408, F.423, H.424, Q.425, E.426 Chain B: S.65, V.67, R.328, A.409, W.410 Ligands: HEM.6, HW0.8 11 PLIP interactions: 1 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:E.426 Hydrogen bonds: B:R.328, B:A.409, B:W.410 Water bridges: B:R.328, B:R.328, B:R.328 pi-Stacking: B:W.410, B:W.410 pi-Cation interactions: B:W.410, B:W.410

2 x HW0: 6-{[(3R,4R)-4-{[5-(6-aminopyridin-2-yl)pentyl]oxy}pyrrolidin-3-yl]methyl}-4-methylpyridin-2-amine(Non-covalent)

HW0.3: 13 residues within 4Å: Chain A: V.67, P.297, V.299, N.301, M.302, W.319, Y.320, E.324, W.410, Y.438 Ligands: HEM.1, H4B.2, ACT.5 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.67, A:V.299, A:W.410 Hydrogen bonds: A:N.301, A:N.301, A:M.321, A:E.324, A:Y.438 Water bridges: A:R.328 pi-Stacking: A:Y.438 HW0.8: 15 residues within 4Å: Chain B: V.67, L.68, Q.210, P.297, V.299, N.301, M.302, W.319, Y.320, E.324, W.410, Y.438 Ligands: HEM.6, H4B.7, ACT.10 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.67, B:V.299, B:W.410 Hydrogen bonds: B:N.301, B:N.301, B:E.324 Water bridges: B:R.328, B:R.328 pi-Stacking: B:Y.438

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

ACT.4: 7 residues within 4Å: Chain A: G.149, I.151, Q.152, W.319, V.381, S.389 Ligands: HEM.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.152 Hydrogen bonds: A:S.389, A:S.389 ACT.5: 5 residues within 4Å: Chain A: Q.210, R.213, N.329, R.335 Ligands: HW0.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.210, A:N.329 Salt bridges: A:R.213, A:R.335 ACT.9: 6 residues within 4Å: Chain B: G.149, I.151, Q.152, W.319, V.381, S.389 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.151, B:Q.152 Hydrogen bonds: B:W.319, B:S.389 ACT.10: 5 residues within 4Å: Chain B: Q.210, R.213, N.329, R.335 Ligands: HW0.8 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.210, B:N.329, B:N.329 Salt bridges: B:R.213, B:R.335

1 x ZN: ZINC ION(Non-covalent)

ZN.11: 5 residues within 4Å: Chain A: C.57, C.62 Chain B: C.57, C.62, G.64 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Metal complexes: A:C.57, A:C.62, B:C.57, B:C.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, H. et al., Mobility of a Conserved Tyrosine Residue Controls Isoform-Dependent Enzyme-Inhibitor Interactions in Nitric Oxide Synthases. Biochemistry (2014)

Release Date

2014-08-13

Peptides

Nitric oxide synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nitric oxide synthase

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