SMTL ID : 7xcl.1

Crystal structure of trimethylamine methyltransferase MttB from Methanosarcina barkeri at 2.5 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-hexamer

Ligands

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: W.142, K.460, D.463, N.467, H.468 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.460, A:K.460, A:D.463 GOL.2: 5 residues within 4Å: Chain A: K.117, Y.118, E.378, H.458, E.462 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.118, A:Y.118, A:E.378 GOL.4: 7 residues within 4Å: Chain B: K.117, Y.118, M.377, E.378, H.458, V.461, E.462 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.118, B:E.378, B:E.378, B:H.458, B:E.462 GOL.5: 6 residues within 4Å: Chain B: W.142, K.460, D.463, V.464, N.467, H.468 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.460, B:D.463 GOL.7: 5 residues within 4Å: Chain C: K.117, Y.118, E.378, H.458, E.462 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.117, C:Y.118, C:E.378, C:H.458, C:E.462 GOL.9: 2 residues within 4Å: Chain D: H.30, R.75 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.75 Water bridges: D:Y.31 GOL.10: 6 residues within 4Å: Chain D: K.117, Y.118, M.377, E.378, H.458, E.462 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Y.118, D:E.378, D:H.458, D:E.462 GOL.11: 5 residues within 4Å: Chain D: W.142, K.460, D.463, N.467, H.468 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:K.460, D:K.460, D:D.463, D:H.468 GOL.13: 5 residues within 4Å: Chain E: W.142, K.460, D.463, N.467, H.468 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:K.460, E:K.460, E:H.468 GOL.14: 6 residues within 4Å: Chain E: K.117, Y.118, M.377, E.378, H.458, E.462 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:Y.118, E:E.378, E:E.462 GOL.16: 6 residues within 4Å: Chain F: K.117, Y.118, M.377, E.378, H.458, E.462 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:E.378

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

NA.3: 5 residues within 4Å: Chain A: L.13, I.397, P.398 Chain F: L.20, E.25 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:E.25, A:I.397 NA.6: 5 residues within 4Å: Chain B: L.13, I.397, P.398 Chain E: L.20, E.25 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain B Hydrogen bonds: E:L.20, B:I.397 NA.8: 4 residues within 4Å: Chain C: L.13, I.397, P.398 Chain D: L.20 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:I.397, C:I.397 NA.12: 5 residues within 4Å: Chain C: L.20, E.25 Chain D: L.13, I.397, P.398 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:I.397, C:E.25 NA.15: 4 residues within 4Å: Chain B: L.20 Chain E: L.13, I.397, P.398 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:E.25, E:I.397 NA.17: 4 residues within 4Å: Chain A: L.20 Chain F: L.13, I.397, P.398 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:I.397, A:E.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, J. et al., Insights into pyrrolysine function from structures of a trimethylamine methyltransferase and its corrinoid protein complex. Commun Biol (2023)

Release Date

2023-01-18

Peptides

Trimethylamine methyltransferase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Trimethylamine methyltransferase

Related Entries With Identical Sequence