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DHFR coordinate geometry with MTX and NDP

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The pinned RCSB 3DFR PDB file reports X-RAY DIFFRACTION at 1.70 Å resolution. Its DBREF row maps chain A residues 1–162 to UniProt P00381. The coordinate rows number MTX as chain A residue 164 and NDP as chain A residue 163. The deposited asymmetric unit contains chain A with these HETATM groups. The PDB header marks the protein as engineered and describes the author-designated biological assembly as monomeric for chain A. COMPND identifies DIHYDROFOLATE REDUCTASE from Lactobacillus casei. HETNAM names MTX METHOTREXATE and NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE. RCSB PDB 3DFR (CC0); primary paper citation: Bolin et al., J. Biol. Chem. volume 257 (1982), PMID 6815178.

What was measured

Each value below is the Euclidean separation between two heavy-atom coordinate positions in the pinned PDB. The second decimal is arithmetic rounding, not an experimental precision statement.

The 3.0 Å native scene contains 19 distance-contact lines, including all 7 listed pairs. Each selected pair appears as a scene contact entity in every frame. The numbers are coordinate measurements; no enzyme-process interpretation is assigned.

MTX coordinate pairs

Each row is a translated pair projection. Full 3D distances: MTX A 164 N1 to Asp A 26 OD1 2.63 angstrom; MTX A 164 NA2 to Asp A 26 OD2 2.88 angstrom; MTX A 164 NA4 to Leu A 4 O 2.69 angstrom; MTX A 164 NA4 to Ala A 97 O 2.89 angstrom; MTX A 164 O1 to Arg A 57 NH1 2.68 angstrom
Each row is independently translated; row placement is schematic. Dashed endpoints retain the common projection's vector and equal scale. Labels are full 3D heavy-atom distances. Largest out-of-page offset: 3.27 Å. Projected/full ratios: MTX A 164 N1 to Asp A 26 OD1 80.4%; MTX A 164 NA2 to Asp A 26 OD2 77.9%; MTX A 164 NA4 to Leu A 4 O 58.5%; MTX A 164 NA4 to Ala A 97 O 98.6%; MTX A 164 O1 to Arg A 57 NH1 51.3%. Two decimal places are arithmetic rounding, not a precision claim.

NDP coordinate pairs

Each row is a translated pair projection. Full 3D distances: NDP A 163 O2A to Thr A 45 OG1 2.61 angstrom; NDP A 163 O1X to Thr A 63 OG1 2.64 angstrom
Each row is independently translated; row placement is schematic. Dashed endpoints retain the common projection's vector and equal scale. Labels are full 3D heavy-atom distances. Largest out-of-page offset: 1.48 Å. Projected/full ratios: NDP A 163 O2A to Thr A 45 OG1 92.3%; NDP A 163 O1X to Thr A 63 OG1 69.3%. Two decimal places are arithmetic rounding, not a precision claim.

PDB records and coordinate limits

The fixed-column file has 1,294 ATOM rows and 345 HETATM rows, including 33 MTX atoms, 48 NDP atoms, and 264 water atoms; 1,375 non-water heavy atoms are retained. It has 1 coordinate model, 81 CONECT rows, 36 SITE rows, and 0 LINK rows. CONECT rows list atom connections within MTX and NDP; none joins a protein atom to either group. These are deposited file annotations, separate from the coordinate measurements. AltLoc alternatives: 0; hydrogen/deuterium coordinate rows: 0; ligand occupancy values: MTX 1.00; NDP 1.00. REMARK 470 lists LYS A 51: CG, CD, CE, NZ as absent. RCSB PDB 3DFR.

What these coordinates do and do not show

This is one static coordinate model. It does not show atoms moving over time or a reaction sequence. The coordinate file contains no hydrogen positions; the heavy-atom separations alone do not locate hydrogen positions. No enzyme function or reaction effect is assigned to any measured distance. RCSB PDB 3DFR; PMID 6815178.

Video: fixed coordinates, rotating camera

Heavy-atom distances are geometric measurements, not inferred bonds. Only the camera turns; no atom moves. At the 3.0 Å cutoff, the green distance marks include the 7 selected MTX and NDP pairs; the scene has 19 contact lines total.

Live: orbit it yourself

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See the measured diagram or video.

Heavy-atom distances are geometric measurements, not inferred bonds. A single static snapshot; no atom moves.

Papers the corpus links to this protein

The corpus links 8 papers across 1 UniProt entry (P00381); per-protein counts: P00381: 8. These papers are cross-referenced by the corpus and are not necessarily about this structure.

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