SMTL ID : 4ew2.2 (1 other biounit)

The structure of human glycinamide ribonucleotide transformylase in complex with 10S-methylthio-DDATHF.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 8 residues within 4Å: Chain A: G.11, S.12, N.13, L.14, Q.15, A.16, K.45, H.174 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.13, A:L.14, A:Q.15, A:A.16 Water bridges: A:H.174, A:H.174, A:H.174 Salt bridges: A:K.45, A:H.174 PO4.5: 8 residues within 4Å: Chain B: G.11, S.12, N.13, L.14, Q.15, A.16, K.45, H.174 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.13, B:L.14, B:Q.15, B:A.16 Water bridges: B:H.174, B:H.174, B:H.174 Salt bridges: B:K.45, B:H.174

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 2 residues within 4Å: Chain A: K.157, R.168 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.157, A:R.168 SO4.3: 5 residues within 4Å: Chain A: N.119, A.120, H.121, E.122, V.162 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.119, A:H.121, A:E.122 Water bridges: A:N.119, A:A.120 Salt bridges: A:H.121 SO4.6: 2 residues within 4Å: Chain B: K.157, R.168 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.157, B:R.168 SO4.7: 5 residues within 4Å: Chain B: N.119, A.120, H.121, E.122, V.162 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.119, B:H.121, B:E.122 Water bridges: B:N.119, B:A.120, B:H.121, B:H.121 Salt bridges: B:H.121

2 x DXY: N-({4-[(1S)-4-(2,4-diamino-6-oxo-1,6-dihydropyrimidin-5-yl)-1-(methylsulfanyl)butyl]phenyl}carbonyl)-L-glutamic acid(Non-covalent)

DXY.4: 13 residues within 4Å: Chain A: R.64, L.85, F.88, M.89, R.90, I.91, L.92, V.97, N.106, V.139, A.140, E.141, V.143 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.85, A:I.91 Hydrogen bonds: A:M.89, A:M.89, A:M.89, A:R.90, A:I.91, A:L.92, A:L.92, A:A.140 Water bridges: A:N.36, A:D.144, A:D.144 Salt bridges: A:R.64, A:R.90, A:R.90 DXY.8: 13 residues within 4Å: Chain B: R.64, L.85, F.88, M.89, R.90, I.91, L.92, V.97, N.106, V.139, A.140, E.141, V.143 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:L.85, B:I.91 Hydrogen bonds: B:M.89, B:M.89, B:M.89, B:R.90, B:I.91, B:L.92, B:L.92, B:A.140 Water bridges: B:N.36, B:D.144, B:D.144 Salt bridges: B:R.64, B:R.90, B:R.90

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Connelly, S. et al., Biological and Structural Evaluation of 10R- and 10S-Methylthio-DDACTHF Reveals a New Role for Sulfur in Inhibition of Glycinamide Ribonucleotide Transformylase. Biochemistry (2013)

Release Date

2013-07-31

Peptides

Trifunctional purine biosynthetic protein adenosine-3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Trifunctional purine biosynthetic protein adenosine-3

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