SMTL ID : 5uos.1

Crystal Structure of CblC (MMACHC) (1-238), a human B12 processing enzyme, complexed with an Antivitamin B12

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.51 Å

Oligo State

monomer

Ligands

1 x B12: COBALAMIN(Non-covalent)

B12.1: 31 residues within 4Å: Chain A: L.37, L.38, P.39, F.42, D.107, P.116, I.118, L.119, A.120, Q.121, T.122, H.125, V.126, Y.132, Q.134, Q.136, R.147, S.149, V.151, C.152, F.161, A.162, I.163, R.164, F.199, N.200, W.203, Y.208, R.209 Ligands: 8FS.2, GSH.3 28 PLIP interactions: 28 interactions with chain A, Hydrophobic interactions: A:L.37, A:L.37, A:P.116, A:Q.121, A:T.122, A:H.125, A:Y.132, A:F.199, A:W.203 Hydrogen bonds: A:D.107, A:I.118, A:A.120, A:Y.132, A:Y.132, A:Q.134, A:Q.134, A:S.149, A:C.152, A:C.152, A:I.163, A:R.209 Water bridges: A:Q.121, A:R.147, A:R.147, A:R.147, A:R.147, A:Y.208 Salt bridges: A:R.147

1 x 8FS: 1-ethynyl-2,4-difluorobenzene(Non-functional Binders)

8FS.2: 2 residues within 4Å: Ligands: B12.1, GSH.3 No protein-ligand interaction detected (PLIP)

1 x GSH: GLUTATHIONE(Non-covalent)

GSH.3: 13 residues within 4Å: Chain A: D.80, P.81, V.82, D.83, F.161, A.162, R.164, R.209, Y.218, F.226, R.233 Ligands: B12.1, 8FS.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:D.80, A:V.82, A:D.83, A:D.83, A:R.164, A:R.164, A:Y.218, A:R.233, A:R.233 Water bridges: A:R.209, A:R.209 Salt bridges: A:R.209

1 x 171: 2-PHENYLAMINO-ETHANESULFONIC ACID(Non-covalent)

171.4: 10 residues within 4Å: Chain A: A.87, L.90, G.91, R.94, I.104, I.105, A.106, Y.108, E.109 Ligands: NA.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.87, A:L.90 Hydrogen bonds: A:E.109

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

SO4.5: 3 residues within 4Å: Chain A: E.139, A.140, D.141 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.140, A:D.141, A:D.141 SO4.6: 4 residues within 4Å: Chain A: A.140, P.142, R.189, I.193 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.189

1 x NA: SODIUM ION(Non-functional Binders)

NA.7: 1 residues within 4Å: Ligands: 171.4 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ruetz, M. et al., Antivitamin B12 Inhibition of the Human B12 -Processing Enzyme CblC: Crystal Structure of an Inactive Ternary Complex with Glutathione as the Cosubstrate. Angew. Chem. Int. Ed. Engl. (2017)

Release Date

2017-06-07

Peptides

Methylmalonic aciduria and homocystinuria type C protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Methylmalonic aciduria and homocystinuria type C protein

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