SMTL ID : 6s6y.2 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

hetero-2-2-2-2-mer

Ligands

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

FMT.1: 3 residues within 4Å: Chain A: G.63, N.64, G.337 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.63 FMT.11: 1 residues within 4Å: Chain B: R.221 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.221, B:R.221, B:Q.225

1 x L6K: (2~{S})-3-[4-[[5-(aminomethyl)furan-3-yl]methoxy]phenyl]-2-(methylamino)propanoic acid(Non-covalent)

L6K.2: 14 residues within 4Å: Chain A: H.229, L.233, G.234, H.258, F.261, T.308, S.310, F.343, V.351, Q.355, D.377, N.380 Ligands: EDO.3, ZN.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.233, A:F.261, A:F.261, A:F.343, A:V.351 Hydrogen bonds: A:G.234, A:H.258, A:N.380

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 5 residues within 4Å: Chain A: L.233, R.315, Q.316, V.341 Ligands: L6K.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.233

4 x ZN: ZINC ION(Non-covalent)

ZN.4: 5 residues within 4Å: Chain A: K.176, H.229, H.258 Ligands: L6K.2, ZN.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.229, A:H.258 ZN.5: 6 residues within 4Å: Chain A: H.59, K.176, I.309, S.310, L.311 Ligands: ZN.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.59 ZN.24: 7 residues within 4Å: Chain E: H.59, K.176, I.178, I.309, S.310, L.311 Ligands: ZN.25 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:H.59 ZN.25: 5 residues within 4Å: Chain E: H.57, K.176, H.229, H.258 Ligands: ZN.24 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:H.229, E:H.258

5 x K: POTASSIUM ION(Non-covalent)

K.6: 2 residues within 4Å: Chain A: D.396, E.423 No protein-ligand interaction detected (PLIP) K.13: 2 residues within 4Å: Chain B: E.190 Chain C: R.175 No protein-ligand interaction detected (PLIP) K.20: 2 residues within 4Å: Chain D: F.129, E.154 No protein-ligand interaction detected (PLIP) K.29: 2 residues within 4Å: Chain H: D.59, K.195 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:D.59, H:K.195 K.30: 2 residues within 4Å: Chain D: K.33 Chain H: E.188 No protein-ligand interaction detected (PLIP)

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

CL.7: 5 residues within 4Å: Chain A: R.346, G.349, P.350, V.351, S.352 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain B: R.250 Chain C: D.69, R.70, Q.88 Ligand excluded by PLIP

7 x DGL: D-GLUTAMIC ACID(Non-covalent)(Non-functional Binders)

DGL.8: 2 residues within 4Å: Chain A: K.326 Ligands: GLU.21 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.326 DGL.10: 6 residues within 4Å: Chain A: K.326, W.328 Chain B: R.201, D.202 Ligands: GLU.9, GLU.15 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: B:D.202, E.9 Salt bridges: A:K.321, A:K.326 DGL.16: 3 residues within 4Å: Ligands: GLU.9, GLU.17, GLU.21 No protein-ligand interaction detected (PLIP) DGL.22: 7 residues within 4Å: Chain C: A.178, R.197 Chain D: R.123, A.132, W.146 Ligands: GLU.17, DGL.23 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Salt bridges: C:R.197, C:K.257, C:K.257, D:R.123 Hydrogen bonds: D:A.132 DGL.23: 10 residues within 4Å: Chain C: R.159, R.160, A.178, G.179 Chain D: A.132, K.133, R.134, R.144 Ligands: GLU.17, DGL.22 9 PLIP interactions: 5 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:A.132, D:R.134, C:R.160, C:G.161, C:G.179 Salt bridges: D:K.133, D:R.134, D:R.144, C:R.160 DGL.26: 5 residues within 4Å: Chain G: R.159 Ligands: GLU.27, GLU.28, DGL.31, IAS.32 2 PLIP interactions: 2 Ligand-Ligand interactions Hydrophobic interactions: E.27 Hydrogen bonds: E.27 DGL.31: 8 residues within 4Å: Chain G: R.197, K.257 Chain H: R.123, A.132, W.146 Ligands: DGL.26, GLU.27, IAS.32 5 PLIP interactions: 3 interactions with chain H, 2 interactions with chain G Hydrophobic interactions: H:W.146 Hydrogen bonds: H:A.132, G:R.197, G:K.257 Salt bridges: H:R.123

6 x GLU: GLUTAMIC ACID(Non-covalent)(Non-functional Binders)

GLU.9: 7 residues within 4Å: Chain A: K.326 Chain C: I.177, R.196, R.197 Ligands: DGL.10, GLU.15, DGL.16 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Ligand interactions Salt bridges: C:R.196, C:R.197 Hydrogen bonds: E.9, E.9 GLU.15: 8 residues within 4Å: Chain A: K.326 Chain B: G.72, R.153, R.201 Chain C: R.196, T.254 Ligands: GLU.9, DGL.10 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B, Salt bridges: C:R.196, B:R.153, B:R.201 GLU.17: 6 residues within 4Å: Chain C: R.159, R.160, A.178 Ligands: DGL.16, DGL.22, DGL.23 3 PLIP interactions: 3 interactions with chain C, Hydrophobic interactions: C:A.178 Hydrogen bonds: C:R.159, C:R.160 GLU.21: 2 residues within 4Å: Ligands: DGL.8, DGL.16 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.124, D:Y.124 GLU.27: 3 residues within 4Å: Ligands: DGL.26, GLU.28, DGL.31 0 PLIP interactions: GLU.28: 5 residues within 4Å: Chain G: I.177, R.196, R.197 Ligands: DGL.26, GLU.27 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Ligand interactions Hydrogen bonds: G:R.197, E.28, E.28 Salt bridges: G:R.196, G:R.197

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

NA.12: 5 residues within 4Å: Chain B: E.36, V.37, S.38, G.315, A.316 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.37, B:S.38, B:S.38, B:A.316

2 x CA: CALCIUM ION(Non-covalent)

CA.18: 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 CA.19: 2 residues within 4Å: Chain D: E.188 Chain H: K.33 No protein-ligand interaction detected (PLIP)

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

IAS.32: 6 residues within 4Å: Chain G: A.178 Chain H: A.132, R.134, R.144 Ligands: DGL.26, DGL.31 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:A.132 Salt bridges: H:R.144

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
I

E
M

B
J

F
N

C
K

G
O

D
L

H
P

Formylmethanofuran dehydrogenase subunit A

Tungsten-containing formylmethanofuran dehydrogenase, subunit B

Formylmethanofuran dehydrogenase subunit C

Formylmethanofuran--tetrahydromethanopterin formyltransferase

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