6THJ | pdb_00006thj

CBDP35 Native structure

PDB DOI: https://doi.org/10.2210/pdb6THJ/pdb

Classification: HYDROLASE
Organism(s): Listeria phage P35
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-11-20 Released: 2020-12-02
Deposition Author(s): Hermoso, J.A., Bartual, S.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.238 (Depositor), 0.240 (DCC)
R-Value Work:
0.196 (Depositor), 0.200 (DCC)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

CBDP35 Native structure

Hermoso, J.A., Bartual, S.G.

To be published.

Macromolecule Content

Total Structure Weight: 197.73 kDa
Atom Count: 15,197
Modeled Residue Count: 1,662
Deposited Residue Count: 1,668
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PlyP35	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	139	Listeria phage P35	Mutation(s): 0 Gene Names: ply
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain CA [auth I] SDF format, chain DA [auth J] SDF format, chain EA [auth J] SDF format, chain FA [auth K] SDF format, chain GA [auth L] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth D] SDF format, chain T [auth E] SDF format, chain U [auth E] SDF format, chain V [auth F] SDF format, chain X [auth G] SDF format, chain Y [auth G] SDF format, chain Z [auth H] SDF format, chain W [auth F] SDF format, chain S [auth D] SDF format, chain BA [auth I] SDF format, chain AA [auth H] MOL2 format, chain CA [auth I] MOL2 format, chain DA [auth J] MOL2 format, chain EA [auth J] MOL2 format, chain FA [auth K] MOL2 format, chain GA [auth L] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth D] MOL2 format, chain T [auth E] MOL2 format, chain U [auth E] MOL2 format, chain V [auth F] MOL2 format, chain X [auth G] MOL2 format, chain Y [auth G] MOL2 format, chain Z [auth H] MOL2 format, chain W [auth F] MOL2 format, chain S [auth D] MOL2 format, chain BA [auth I] MOL2 format, chain AA [auth H] mmCIF format, chain CA [auth I] mmCIF format, chain DA [auth J] mmCIF format, chain EA [auth J] mmCIF format, chain FA [auth K] mmCIF format, chain GA [auth L] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth D] mmCIF format, chain T [auth E] mmCIF format, chain U [auth E] mmCIF format, chain V [auth F] mmCIF format, chain X [auth G] mmCIF format, chain Y [auth G] mmCIF format, chain Z [auth H] mmCIF format, chain W [auth F] mmCIF format, chain S [auth D] mmCIF format, chain BA [auth I] mmCIF format, chain AA [auth H]	AA [auth H] BA [auth I] CA [auth I] DA [auth J] EA [auth J] AA [auth H], BA [auth I], CA [auth I], DA [auth J], EA [auth J], FA [auth K], GA [auth L], M [auth A], N [auth A], O [auth B], P [auth C], Q [auth C], R [auth D], S [auth D], T [auth E], U [auth E], V [auth F], W [auth F], X [auth G], Y [auth G], Z [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth H] Focus chain BA [auth I] Focus chain CA [auth I] Focus chain DA [auth J] Focus chain EA [auth J] Focus chain FA [auth K] Focus chain GA [auth L] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth E] Focus chain U [auth E] Focus chain V [auth F] Focus chain W [auth F] Focus chain X [auth G] Focus chain Y [auth G] Focus chain Z [auth H] Interactions & Density Focus chain AA [auth H] Focus chain BA [auth I] Focus chain CA [auth I] Focus chain DA [auth J] Focus chain EA [auth J] Focus chain FA [auth K] Focus chain GA [auth L] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth E] Focus chain U [auth E] Focus chain V [auth F] Focus chain W [auth F] Focus chain X [auth G] Focus chain Y [auth G] Focus chain Z [auth H]