SMTL ID : 3njr.1 (1 other biounit)

Crystal structure of C-terminal domain of precorrin-6Y C5,15-methyltransferase from Rhodobacter capsulatus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-tetramer

Ligands

4 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.1: 20 residues within 4Å: Chain A: Q.37, I.38, T.39, G.63, G.64, G.65, S.66, G.67, S.68, I.83, E.84, P.85, R.89, G.111, T.112, A.113, F.127, G.129, G.130, G.131 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:T.39, A:T.39, A:T.39, A:T.39, A:S.66, A:G.67, A:S.68, A:R.89, A:R.89, A:A.113, A:A.113, A:G.131 SAH.3: 17 residues within 4Å: Chain B: Q.37, I.38, T.39, G.63, G.64, G.65, S.66, G.67, S.68, V.69, E.84, P.85, R.89, T.112, A.113, G.130, G.131 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:T.39, B:T.39, B:T.39, B:T.39, B:G.63, B:G.65, B:S.66, B:G.67, B:S.68, B:V.69, B:R.89, B:R.89, B:A.113, B:A.113 SAH.6: 20 residues within 4Å: Chain C: Q.37, I.38, T.39, G.63, G.64, G.65, S.66, G.67, S.68, I.83, E.84, P.85, R.89, G.111, T.112, A.113, F.127, G.129, G.130, G.131 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:T.39, C:T.39, C:T.39, C:S.66, C:G.67, C:S.68, C:R.89, C:R.89, C:A.113, C:A.113, C:G.131 SAH.8: 17 residues within 4Å: Chain D: Q.37, I.38, T.39, G.63, G.64, G.65, S.66, G.67, S.68, V.69, E.84, P.85, R.89, T.112, A.113, G.130, G.131 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:T.39, D:T.39, D:T.39, D:G.63, D:G.65, D:S.66, D:G.67, D:S.68, D:V.69, D:R.89, D:R.89, D:A.113, D:A.113

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: L.157, E.160, R.176, P.196 Chain B: W.191 Chain C: W.191 Chain D: E.160 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:W.191, D:E.160 GOL.5: 5 residues within 4Å: Chain B: K.40, P.42, I.179, Q.181, S.192 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.192 GOL.7: 7 residues within 4Å: Chain A: W.191 Chain B: E.160 Chain C: L.157, E.160, R.176, P.196 Chain D: W.191 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.160, A:W.191 GOL.10: 5 residues within 4Å: Chain D: K.40, P.42, I.179, Q.181, S.192 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.192

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.4: 7 residues within 4Å: Chain B: S.30, A.31, F.32, A.33, H.34, T.99, Y.100 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.34, B:H.34 PG4.9: 7 residues within 4Å: Chain D: S.30, A.31, F.32, A.33, H.34, T.99, Y.100 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:H.34, D:H.34

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Deery, E. et al., An enzyme-trap approach allows isolation of intermediates in cobalamin biosynthesis. Nat.Chem.Biol. (2012)

Release Date

2011-06-08

Peptides

Precorrin-6y methylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Precorrin-6y methylase

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