5T61

TUNGSTEN-CONTAINING FORMYLMETHANOFURAN DEHYDROGENASE FROM METHANOTHERMOBACTER WOLFEII, TRICLINIC FORM AT 2.55 A

Structural Biology Knowledgebase: 5T61 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.259
  • R-Value Work: 0.229

Literature

Macromolecules
Sequence Display for 5T61

Classification: OXIDOREDUCTASE

Total Structure Weight: 1667212.75

Macromolecule Entities
Molecule Chains Length Organism Details
Tungsten formylmethanofuran dehydrogenase subunit fwdA A, G, M..., S, Y, e, k, qA, G, M, S, Y, e, k, q 569 Methanothermobacter wolfeii Details: FwdA subunit contains a carboxylysine at position 178
Tungsten formylmethanofuran dehydrogenase subunit B B, H, N..., T, Z, f, l, rB, H, N, T, Z, f, l, r 432 Methanothermobacter sp. cat2
Tungsten-containing formylmethanofuran dehydrogenase 2 subunit C C, I, O..., U, a, g, m, sC, I, O, U, a, g, m, s 270 Methanothermobacter wolfeii EC#: 1.2.99.5 IUBMB
Tungsten formylmethanofuran dehydrogenase subunit fwdD D, J, P..., V, b, h, n, tD, J, P, V, b, h, n, t 130 Methanothermobacter wolfeii
Tungsten formylmethanofuran dehydrogenase subunit fwdG E, K, Q..., W, c, i, o, uE, K, Q, W, c, i, o, u 82 Methanothermobacter wolfeii
Tungsten formylmethanofuran dehydrogenase subunit fwdF F, L, R..., X, d, j, p, vF, L, R, X, d, j, p, v 349 Methanothermobacter wolfeii

Small Molecules
Ligands 10 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
MFN
Query on MFN

A, G, M, S, Y, e, k, q N-[4,5,7-TRICARBOXYHEPTANOYL]-L-GAMMA-GLUTAMYL- N-{2-[4-({5-[(FORMYLAMINO)METHYL]-3-FURYL}METHOXY)PHENYL]ETHYL}- D-GLUTAMINE
C35 H44 N4 O16
RGBIJPWAWLXPOC-XRVZLLLRSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MGD
Query on MGD

B, H, N, T, Z, f, l, r 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9- TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN- 4-ONE GUANOSINE DINUCLEOTIDE
MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE (Synonym)
C20 H26 N10 O13 P2 S2
VQAGYJCYOLHZDH-ILXWUORBSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SF4
Query on SF4

B, E, F, H, K, L, N, Q, R, T, W, X, Z, c, d, f, i, j, l, o, p, r, u, v IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
W
Query on W

B, H, N, T, Z, f, l, r TUNGSTEN ION
W
FZFRVZDLZISPFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, G, M, S, Y, e, k, q ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

A, B, E, F, G, K, L, M, N, Q, R, S, T, X, Y, Z, c, d, e, i, j, k, o, p, q, r, u, v POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

N CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
H2S
Query on H2S

B, H, N, T, Z, f, l, r HYDROSULFURIC ACID
HYDROGEN SULFIDE (Synonym)
H2 S
RWSOTUBLDIXVET-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

B, H, O, T, Z, f, l, r MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A, G, M, S, e, k, q SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
KCX
Query on KCX
A, G, M, S, Y, e, k, q L-PEPTIDE LINKING C7 H14 N2 O4 LYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.259
  • R-Value Work: 0.229
  • Space Group: P 1

Unit Cell:

Length (Å) Angle (°)
a = 174.18 α = 89.98
b = 173.68 β = 95.42
c = 183.16 γ = 92.14

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2016-09-01
  • Released Date: 2016-10-19
  • Deposition author(s): Wagner, T., Ermler, U., Shima, S.

Revision History

  • 2016-12-21
    Type: Citation | Details: Citation