lmnature · Molecular biology · Page 11

Biotin inside one streptavidin barrel

Media on this page: text, diagram, video and live animation are available.

The pinned RCSB PDB 1STP coordinate file records streptavidin from Streptomyces avidinii with one non-water HETATM component, BTN A 300, identified as biotin. The entry reports X-ray diffraction at 2.60 Å resolution. The primary citation is Weber et al. (1989), Science 243, 85–88, PMID 2911722 (DOI).

The asymmetric-unit coordinates contain one engineered chain A, with modeled residues 13–133 (121 coordinate residues); SEQRES lists 159 residues and DBREF maps the sequence to UniProt P22629, residues 25–183. BTN A 300 has 16 heavy atoms. The RCSB assembly record describes biological assembly 1 as an A4 homotetramer with D2 symmetry, generated from chain A. This page and video show only the deposited asymmetric unit, without symmetry-generated copies. PDB coordinate files are available under CC0 1.0.

The file contains 84 water atoms; 71 have occupancy below 1.00. The selected protein and BTN atoms all have occupancy 1.00. The file has no alternate-location records or hydrogen atoms; the video renderer omits water. Its COMPND record marks the protein as engineered.

What was measured

Each value is a heavy-atom distance recomputed from the deposited coordinates. Tyr43 OH to BTN 300 O3: 2.58 Å; Ser88 OG to BTN 300 O11: 2.69 Å; Ser27 OG to BTN 300 O3: 2.77 Å; Asp128 OD2 to BTN 300 N1: 2.78 Å; Asn49 N to BTN 300 O12: 2.95 Å; Asn23 ND2 to BTN 300 O3: 2.99 Å. Values are rounded to two decimals for display; these are coordinate distances, not bonds.

B-factors (protein atom / BTN atom, Ų): Tyr 43 OH / BTN 300 O3: 17.51 / 17.93; Ser 88 OG / BTN 300 O11: 16.41 / 21.65; Ser 27 OG / BTN 300 O3: 21.28 / 17.93; Asp 128 OD2 / BTN 300 N1: 14.45 / 17.73; Asn 49 N / BTN 300 O12: 21.07 / 22.67; Asn 23 ND2 / BTN 300 O3: 18.49 / 17.93. The structure resolution is 2.60 Å; the second decimal is arithmetic formatting, not measurement certainty.

Six independent measured heavy-atom distances: Tyr43 OH to BTN 300 O3: 2.58 Å; Ser88 OG to BTN 300 O11: 2.69 Å; Ser27 OG to BTN 300 O3: 2.77 Å; Asp128 OD2 to BTN 300 N1: 2.78 Å; Asn49 N to BTN 300 O12: 2.95 Å; Asn23 ND2 to BTN 300 O3: 2.99 Å. Each row has its own orientation; rows do not encode relative positions.
Each row is a separate local view of one atom pair; row placement does not show relative positions. Labels are full three-dimensional distances.

What the coordinate file records

The file has 0 LINK records. Its 16 CONECT records describe atom pairs within BTN; none joins a protein atom to BTN. The distances here were independently calculated from coordinates, not from those records. SITE AC1 lists 15 residue entries.

This is one static coordinate model. It does not show atom motion, a process over time, or the other subunits in the RCSB biological assembly.

Video: the chain and BTN coordinates

Heavy-atom distances are geometric measurements, not inferred bonds. Only the camera turns; no atom moves. At the 3.0 Å cutoff, the six selected protein–BTN distance pairs appear in the overlay.

Rendered with public lmvideo v0.1.126 from videos/mb11.lms. The fidelity table and rendered scene-entity IDs are recorded in durable-memory/video-provenance.md.

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 9 papers across 1 UniProt entry (P22629); per-protein counts: P22629: 9. These papers are cross-referenced by the corpus and are not necessarily about this structure.

Titles, journal and year load from Europe PMC when JavaScript is available.