SMTL ID : 6s6y.1 (1 other biounit)

X-ray crystal structure of the formyltransferase/hydrolase complex (FhcABCD) from Methylorubrum extorquens in complex with methylofuran

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

hetero-2-2-2-2-mer

Ligands

1 x FMT: FORMIC ACID(Non-functional Binders)

FMT.1: 3 residues within 4Å: Chain A: G.63, N.64, S.331 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.331

1 x MFN: N-[4,5,7-TRICARBOXYHEPTANOYL]-L-GAMMA-GLUTAMYL-N-{2-[4-({5-[(FORMYLAMINO)METHYL]-3-FURYL}METHOXY)PHENYL]ETHYL}-D-GLUTAMINE(Non-covalent)

MFN.2: 12 residues within 4Å: Chain A: H.229, L.233, H.258, F.261, T.308, S.310, F.343, Y.345, Q.355, D.377, N.380 Ligands: ZN.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.233, A:N.380 Hydrogen bonds: A:H.258, A:N.380 pi-Stacking: A:F.261, A:F.343

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: D.128, P.130, W.492, F.493 Chain B: R.41, R.45 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.128, A:W.492, B:R.41, B:R.41 GOL.25: 7 residues within 4Å: Chain H: V.49, E.55, F.81, G.169, G.170, V.253, D.255 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:D.255

4 x ZN: ZINC ION(Non-covalent)

ZN.4: 6 residues within 4Å: Chain A: H.59, K.176, I.309, S.310, L.311 Ligands: ZN.5 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.59 ZN.5: 6 residues within 4Å: Chain A: K.176, H.229, H.258, S.310 Ligands: MFN.2, ZN.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.229, A:H.258 ZN.23: 5 residues within 4Å: Chain E: K.176, H.229, H.258, S.310 Ligands: ZN.24 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:H.258 ZN.24: 6 residues within 4Å: Chain E: H.59, K.176, I.178, S.310, L.311 Ligands: ZN.23 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:H.59

4 x CA: CALCIUM ION(Non-covalent)

CA.6: 1 residues within 4Å: Chain A: E.218 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.218, A:E.218 CA.7: 2 residues within 4Å: Chain A: E.398, E.423 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.398, A:E.423 CA.8: 2 residues within 4Å: Chain A: S.117, D.334 No protein-ligand interaction detected (PLIP) CA.13: 3 residues within 4Å: Chain B: E.65, D.216, R.221 No protein-ligand interaction detected (PLIP)

4 x K: POTASSIUM ION(Non-covalent)

K.9: 1 residues within 4Å: Chain A: D.463 No protein-ligand interaction detected (PLIP) K.10: 2 residues within 4Å: Chain A: E.399, D.465 No protein-ligand interaction detected (PLIP) K.20: 2 residues within 4Å: Chain D: D.59, K.195 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.59, D:K.195 K.26: 3 residues within 4Å: Chain H: D.59, K.195, A.196 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:D.59, H:K.195

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.11: 4 residues within 4Å: Chain A: N.285, E.289, S.367, R.371 Ligand excluded by PLIP CL.12: 1 residues within 4Å: Chain A: K.208 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain B: R.250 Chain C: D.69, R.70, Q.88 Ligand excluded by PLIP

3 x DGL: D-GLUTAMIC ACID(Non-covalent)

DGL.14: 8 residues within 4Å: Chain A: K.326 Chain B: A.71, R.153, R.201 Chain C: R.196, T.254 Ligands: NH2.15, GLU.19 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Salt bridges: B:R.153, B:K.157, B:R.201, C:R.196 DGL.17: 4 residues within 4Å: Chain C: R.159 Ligands: GLU.18, DGL.21, IAS.22 3 PLIP interactions: 3 Ligand-Ligand interactions Hydrophobic interactions: E.18 Hydrogen bonds: E.18, E.18 DGL.21: 7 residues within 4Å: Chain C: R.197 Chain D: R.123, A.132, W.146 Ligands: DGL.17, GLU.18, IAS.22 5 PLIP interactions: 1 Ligand-Ligand interactions, 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: E.18, D:A.132, C:K.257 Hydrophobic interactions: D:W.146 Salt bridges: D:R.123

1 x NH2: AMINO GROUP(Non-functional Binders)

NH2.15: 2 residues within 4Å: Chain A: K.326 Ligands: DGL.14 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.326

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.18: 4 residues within 4Å: Chain C: R.159 Ligands: DGL.17, GLU.19, DGL.21 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Salt bridges: A:K.326 Hydrogen bonds: C:R.159 GLU.19: 5 residues within 4Å: Chain C: I.177, R.196, R.197 Ligands: DGL.14, GLU.18 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Ligand interactions Salt bridges: C:R.196, C:R.197 Hydrogen bonds: E.19

1 x IAS: BETA-L-ASPARTIC ACID(Non-covalent)

IAS.22: 8 residues within 4Å: Chain C: R.159, R.160, A.178 Chain D: A.132, R.134, R.144 Ligands: DGL.17, DGL.21 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:A.132 Salt bridges: D:R.134, D:R.144 Hydrophobic interactions: C:A.178

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hemmann, J.L. et al., Methylofuran is a prosthetic group of the formyltransferase/hydrolase complex and shuttles one-carbon units between two active sites. Proc.Natl.Acad.Sci.USA (2019)

Release Date

2019-12-04

Peptides

Formylmethanofuran dehydrogenase subunit A: AE
Tungsten-containing formylmethanofuran dehydrogenase, subunit B: BF
Formylmethanofuran dehydrogenase subunit C: CG
Formylmethanofuran--tetrahydromethanopterin formyltransferase: DH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

B
B

F
F

C
C

G
G

D
D

H
H

Formylmethanofuran dehydrogenase subunit A

Tungsten-containing formylmethanofuran dehydrogenase, subunit B

Formylmethanofuran dehydrogenase subunit C

Formylmethanofuran--tetrahydromethanopterin formyltransferase

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