1RTM

TRIMERIC STRUCTURE OF A C-TYPE MANNOSE-BINDING PROTEIN

PDB DOI: https://doi.org/10.2210/pdb1RTM/pdb

Classification: LECTIN
Organism(s): Rattus norvegicus
Mutation(s): No

Deposited: 1994-11-21 Released: 1995-02-07
Deposition Author(s): Weis, W.I., Drickamer, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.270
R-Value Work: 0.220
R-Value Observed: 0.220

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Trimeric structure of a C-type mannose-binding protein.

Weis, W.I., Drickamer, K.

(1994) Structure 2: 1227-1240

PubMed: 7704532 Search on PubMed
DOI: https://doi.org/10.1016/S0969-2126(94)00124-3
Primary Citation of Related Structures:
1RTM

PubMed Abstract:
Mannose-binding proteins (MBPs) are C-type (Ca(2+)-dependent) animal lectins found in serum. They recognize cell-surface oligosaccharide structures characteristic of pathogenic bacteria and fungi, and trigger the neutralization of these organisms. Like most lectins, MBPs display weak intrinsic affinity for monovalent sugar ligands, but bind avidly to multivalent ligands.

Organizational Affiliation

Department of Structural Biology, Stanford University School of Medicine, CA 94305.

Macromolecule Content

Total Structure Weight: 51.28 kDa
Atom Count: 4,061
Modelled Residue Count: 447
Deposited Residue Count: 447
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MANNOSE-BINDING PROTEIN-A	A [auth 1], B [auth 2], C [auth 3]	149	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for P19999 (Rattus norvegicus) Explore P19999 Go to UniProtKB: P19999
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P19999
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain BA [auth 3] SDF format, chain CA [auth 3] SDF format, chain DA [auth 3] SDF format, chain H [auth 1] SDF format, chain I [auth 1] SDF format, chain J [auth 1] SDF format, chain K [auth 1] SDF format, chain L [auth 1] SDF format, chain M [auth 1] SDF format, chain N [auth 1] SDF format, chain O [auth 1] SDF format, chain P [auth 1] SDF format, chain U [auth 2] SDF format, chain V [auth 2] SDF format, chain W [auth 2] MOL2 format, chain BA [auth 3] MOL2 format, chain CA [auth 3] MOL2 format, chain DA [auth 3] MOL2 format, chain H [auth 1] MOL2 format, chain I [auth 1] MOL2 format, chain J [auth 1] MOL2 format, chain K [auth 1] MOL2 format, chain L [auth 1] MOL2 format, chain M [auth 1] MOL2 format, chain N [auth 1] MOL2 format, chain O [auth 1] MOL2 format, chain P [auth 1] MOL2 format, chain U [auth 2] MOL2 format, chain V [auth 2] MOL2 format, chain W [auth 2]	BA [auth 3] CA [auth 3] DA [auth 3] H [auth 1] I [auth 1] BA [auth 3], CA [auth 3], DA [auth 3], H [auth 1], I [auth 1], J [auth 1], K [auth 1], L [auth 1], M [auth 1], N [auth 1], O [auth 1], P [auth 1], U [auth 2], V [auth 2], W [auth 2]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth 3] Focus chain CA [auth 3] Focus chain DA [auth 3] Focus chain H [auth 1] Focus chain I [auth 1] Focus chain J [auth 1] Focus chain K [auth 1] Focus chain L [auth 1] Focus chain M [auth 1] Focus chain N [auth 1] Focus chain O [auth 1] Focus chain P [auth 1] Focus chain U [auth 2] Focus chain V [auth 2] Focus chain W [auth 2] Interactions & Density Focus chain BA [auth 3] Focus chain CA [auth 3] Focus chain DA [auth 3] Focus chain H [auth 1] Focus chain I [auth 1] Focus chain J [auth 1] Focus chain K [auth 1] Focus chain L [auth 1] Focus chain M [auth 1] Focus chain N [auth 1] Focus chain O [auth 1] Focus chain P [auth 1] Focus chain U [auth 2] Focus chain V [auth 2] Focus chain W [auth 2]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain D [auth 1] SDF format, chain E [auth 1] SDF format, chain F [auth 1] SDF format, chain Q [auth 2] SDF format, chain R [auth 2] SDF format, chain S [auth 2] SDF format, chain X [auth 3] SDF format, chain Y [auth 3] SDF format, chain Z [auth 3] MOL2 format, chain D [auth 1] MOL2 format, chain E [auth 1] MOL2 format, chain F [auth 1] MOL2 format, chain Q [auth 2] MOL2 format, chain R [auth 2] MOL2 format, chain S [auth 2] MOL2 format, chain X [auth 3] MOL2 format, chain Y [auth 3] MOL2 format, chain Z [auth 3]	D [auth 1] E [auth 1] F [auth 1] Q [auth 2] R [auth 2] D [auth 1], E [auth 1], F [auth 1], Q [auth 2], R [auth 2], S [auth 2], X [auth 3], Y [auth 3], Z [auth 3]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth 1] Focus chain E [auth 1] Focus chain F [auth 1] Focus chain Q [auth 2] Focus chain R [auth 2] Focus chain S [auth 2] Focus chain X [auth 3] Focus chain Y [auth 3] Focus chain Z [auth 3] Interactions & Density Focus chain D [auth 1] Focus chain E [auth 1] Focus chain F [auth 1] Focus chain Q [auth 2] Focus chain R [auth 2] Focus chain S [auth 2] Focus chain X [auth 3] Focus chain Y [auth 3] Focus chain Z [auth 3]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth 3] SDF format, chain G [auth 1] SDF format, chain T [auth 2] MOL2 format, chain AA [auth 3] MOL2 format, chain G [auth 1] MOL2 format, chain T [auth 2]	AA [auth 3], G [auth 1], T [auth 2]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth 3] Focus chain G [auth 1] Focus chain T [auth 2] Interactions & Density Focus chain AA [auth 3] Focus chain G [auth 1] Focus chain T [auth 2]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.270
R-Value Work: 0.220
R-Value Observed: 0.220
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80	α = 90
b = 85.1	β = 106.3
c = 98.5	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 1995-02-07

Deposition Author(s):

Weis, W.I.

Drickamer, K.

Revision History (Full details and data files)

Version 1.0: 1995-02-07
Type: Initial release
Version 1.1: 2008-03-03
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance