7ANY

Structure of the Laspartomycin C Friulimicin-like mutant in complex with Geranyl phosphate

PDB DOI: https://doi.org/10.2210/pdb7ANY/pdb

Classification: ANTIBIOTIC
Organism(s): Streptomyces viridochromogenes
Mutation(s): No

Deposited: 2020-10-13 Released: 2022-02-02
Deposition Author(s): Zeronian, M.R., Pearce, N.M., Lutz, M., Wood, T.M., Martin, N.I., Janssen, B.J.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.14 Å
R-Value Free: 0.192
R-Value Work: 0.160
R-Value Observed: 0.161

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Mechanistic insights into the C55-P targeting lipopeptide antibiotics revealed by structure-activity studies and high-resolution crystal structures

Wood, T.M., Zeronian, M.R., Buijs, N., Bertheussen, K., Abedian, H.K., Johnson, A.V., Pearce, N.M., Lutz, M., Kemmink, J., Seirsma, T., Hamoen, L.W., Janssen, B.J.C., Martin, N.I.

(2022) Chem Sci 13: 2985-2991

DOI: https://doi.org/10.1039/D1SC07190D

Macromolecule Content

Total Structure Weight: 20.88 kDa
Atom Count: 1,493
Modelled Residue Count: 144
Deposited Residue Count: 144
Unique protein chains: 1

Macromolecules

Find similar proteins by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Laspartomycin C Friulimicin-like mutant	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	12	Streptomyces viridochromogenes	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RDZ Query on RDZ Download Ideal Coordinates CCD File SDF format, chain DC [auth L] SDF format, chain EB [auth H] SDF format, chain HA [auth D] SDF format, chain JB [auth I] SDF format, chain O [auth A] SDF format, chain OA [auth E] SDF format, chain PB [auth J] SDF format, chain T [auth B] SDF format, chain TA [auth F] SDF format, chain Y [auth C] SDF format, chain YB [auth K] SDF format, chain ZA [auth G] MOL2 format, chain DC [auth L] MOL2 format, chain EB [auth H] MOL2 format, chain HA [auth D] MOL2 format, chain JB [auth I] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth E] MOL2 format, chain PB [auth J] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth F] MOL2 format, chain Y [auth C] MOL2 format, chain YB [auth K] MOL2 format, chain ZA [auth G]	DC [auth L] EB [auth H] HA [auth D] JB [auth I] O [auth A] DC [auth L], EB [auth H], HA [auth D], JB [auth I], O [auth A], OA [auth E], PB [auth J], T [auth B], TA [auth F], Y [auth C], YB [auth K], ZA [auth G]	Geranyl phosphate C₁₀ H₁₉ O₄ P FFOWJDCTFSWUMJ-JXMROGBWSA-N		Interactions Focus chain DC [auth L] Focus chain EB [auth H] Focus chain HA [auth D] Focus chain JB [auth I] Focus chain O [auth A] Focus chain OA [auth E] Focus chain PB [auth J] Focus chain T [auth B] Focus chain TA [auth F] Focus chain Y [auth C] Focus chain YB [auth K] Focus chain ZA [auth G] Interactions & Density Focus chain DC [auth L] Focus chain EB [auth H] Focus chain HA [auth D] Focus chain JB [auth I] Focus chain O [auth A] Focus chain OA [auth E] Focus chain PB [auth J] Focus chain T [auth B] Focus chain TA [auth F] Focus chain Y [auth C] Focus chain YB [auth K] Focus chain ZA [auth G]
CD Query on CD Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain GA [auth D] SDF format, chain RB [auth J] MOL2 format, chain AA [auth C] MOL2 format, chain GA [auth D] MOL2 format, chain RB [auth J]	AA [auth C], GA [auth D], RB [auth J]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain GA [auth D] Focus chain RB [auth J] Interactions & Density Focus chain AA [auth C] Focus chain GA [auth D] Focus chain RB [auth J]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain AB [auth G] SDF format, chain BA [auth C] SDF format, chain BC [auth L] SDF format, chain CB [auth H] SDF format, chain CC [auth L] SDF format, chain DB [auth H] SDF format, chain EA [auth D] SDF format, chain EC [auth L] SDF format, chain FA [auth D] SDF format, chain FB [auth H] SDF format, chain HB [auth I] SDF format, chain IA [auth D] SDF format, chain IB [auth I] SDF format, chain JA [auth D] SDF format, chain KA [auth D] SDF format, chain KB [auth I] SDF format, chain LB [auth I] SDF format, chain M [auth A] SDF format, chain MA [auth E] SDF format, chain N [auth A] SDF format, chain NA [auth E] SDF format, chain NB [auth J] SDF format, chain OB [auth J] SDF format, chain P [auth A] SDF format, chain PA [auth E] SDF format, chain QB [auth J] SDF format, chain R [auth B] SDF format, chain RA [auth F] SDF format, chain S [auth B] SDF format, chain SA [auth F] SDF format, chain SB [auth J] SDF format, chain U [auth B] SDF format, chain UA [auth F] SDF format, chain VA [auth F] SDF format, chain W [auth C] SDF format, chain WB [auth K] SDF format, chain X [auth C] SDF format, chain XA [auth G] SDF format, chain XB [auth K] SDF format, chain YA [auth G] SDF format, chain Z [auth C] SDF format, chain ZB [auth K] MOL2 format, chain AB [auth G] MOL2 format, chain BA [auth C] MOL2 format, chain BC [auth L] MOL2 format, chain CB [auth H] MOL2 format, chain CC [auth L] MOL2 format, chain DB [auth H] MOL2 format, chain EA [auth D] MOL2 format, chain EC [auth L] MOL2 format, chain FA [auth D] MOL2 format, chain FB [auth H] MOL2 format, chain HB [auth I] MOL2 format, chain IA [auth D] MOL2 format, chain IB [auth I] MOL2 format, chain JA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain KB [auth I] MOL2 format, chain LB [auth I] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth E] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth E] MOL2 format, chain NB [auth J] MOL2 format, chain OB [auth J] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth E] MOL2 format, chain QB [auth J] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth F] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth F] MOL2 format, chain SB [auth J] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth F] MOL2 format, chain VA [auth F] MOL2 format, chain W [auth C] MOL2 format, chain WB [auth K] MOL2 format, chain X [auth C] MOL2 format, chain XA [auth G] MOL2 format, chain XB [auth K] MOL2 format, chain YA [auth G] MOL2 format, chain Z [auth C] MOL2 format, chain ZB [auth K]	AB [auth G] BA [auth C] BC [auth L] CB [auth H] CC [auth L] AB [auth G], BA [auth C], BC [auth L], CB [auth H], CC [auth L], DB [auth H], EA [auth D], EC [auth L], FA [auth D], FB [auth H], HB [auth I], IA [auth D], IB [auth I], JA [auth D], KA [auth D], KB [auth I], LB [auth I], M [auth A], MA [auth E], N [auth A], NA [auth E], NB [auth J], OB [auth J], P [auth A], PA [auth E], QB [auth J], R [auth B], RA [auth F], S [auth B], SA [auth F], SB [auth J], U [auth B], UA [auth F], VA [auth F], W [auth C], WB [auth K], X [auth C], XA [auth G], XB [auth K], YA [auth G], Z [auth C], ZB [auth K]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AB [auth G] Focus chain BA [auth C] Focus chain BC [auth L] Focus chain CB [auth H] Focus chain CC [auth L] Focus chain DB [auth H] Focus chain EA [auth D] Focus chain EC [auth L] Focus chain FA [auth D] Focus chain FB [auth H] Focus chain HB [auth I] Focus chain IA [auth D] Focus chain IB [auth I] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain KB [auth I] Focus chain LB [auth I] Focus chain M [auth A] Focus chain MA [auth E] Focus chain N [auth A] Focus chain NA [auth E] Focus chain NB [auth J] Focus chain OB [auth J] Focus chain P [auth A] Focus chain PA [auth E] Focus chain QB [auth J] Focus chain R [auth B] Focus chain RA [auth F] Focus chain S [auth B] Focus chain SA [auth F] Focus chain SB [auth J] Focus chain U [auth B] Focus chain UA [auth F] Focus chain VA [auth F] Focus chain W [auth C] Focus chain WB [auth K] Focus chain X [auth C] Focus chain XA [auth G] Focus chain XB [auth K] Focus chain YA [auth G] Focus chain Z [auth C] Focus chain ZB [auth K] Interactions & Density Focus chain AB [auth G] Focus chain BA [auth C] Focus chain BC [auth L] Focus chain CB [auth H] Focus chain CC [auth L] Focus chain DB [auth H] Focus chain EA [auth D] Focus chain EC [auth L] Focus chain FA [auth D] Focus chain FB [auth H] Focus chain HB [auth I] Focus chain IA [auth D] Focus chain IB [auth I] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain KB [auth I] Focus chain LB [auth I] Focus chain M [auth A] Focus chain MA [auth E] Focus chain N [auth A] Focus chain NA [auth E] Focus chain NB [auth J] Focus chain OB [auth J] Focus chain P [auth A] Focus chain PA [auth E] Focus chain QB [auth J] Focus chain R [auth B] Focus chain RA [auth F] Focus chain S [auth B] Focus chain SA [auth F] Focus chain SB [auth J] Focus chain U [auth B] Focus chain UA [auth F] Focus chain VA [auth F] Focus chain W [auth C] Focus chain WB [auth K] Focus chain X [auth C] Focus chain XA [auth G] Focus chain XB [auth K] Focus chain YA [auth G] Focus chain Z [auth C] Focus chain ZB [auth K]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AC [auth K] SDF format, chain BB [auth G] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain FC [auth L] SDF format, chain GB [auth H] SDF format, chain LA [auth D] SDF format, chain MB [auth I] SDF format, chain Q [auth A] SDF format, chain QA [auth E] SDF format, chain UB [auth J] SDF format, chain V [auth B] SDF format, chain VB [auth J] SDF format, chain WA [auth F] MOL2 format, chain AC [auth K] MOL2 format, chain BB [auth G] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain FC [auth L] MOL2 format, chain GB [auth H] MOL2 format, chain LA [auth D] MOL2 format, chain MB [auth I] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth E] MOL2 format, chain UB [auth J] MOL2 format, chain V [auth B] MOL2 format, chain VB [auth J] MOL2 format, chain WA [auth F]	AC [auth K] BB [auth G] CA [auth C] DA [auth C] FC [auth L] AC [auth K], BB [auth G], CA [auth C], DA [auth C], FC [auth L], GB [auth H], LA [auth D], MB [auth I], Q [auth A], QA [auth E], UB [auth J], V [auth B], VB [auth J], WA [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AC [auth K] Focus chain BB [auth G] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain FC [auth L] Focus chain GB [auth H] Focus chain LA [auth D] Focus chain MB [auth I] Focus chain Q [auth A] Focus chain QA [auth E] Focus chain UB [auth J] Focus chain V [auth B] Focus chain VB [auth J] Focus chain WA [auth F] Interactions & Density Focus chain AC [auth K] Focus chain BB [auth G] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain FC [auth L] Focus chain GB [auth H] Focus chain LA [auth D] Focus chain MB [auth I] Focus chain Q [auth A] Focus chain QA [auth E] Focus chain UB [auth J] Focus chain V [auth B] Focus chain VB [auth J] Focus chain WA [auth F]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain TB [auth J] MOL2 format, chain TB [auth J]	TB [auth J]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain TB [auth J] Interactions & Density Focus chain TB [auth J]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
2RA Query on 2RA	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	D-PEPTIDE LINKING	C₃ H₈ N₂ O₂		ALA
DNP Query on DNP	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	L-PEPTIDE LINKING	C₃ H₉ N₂ O₂		ALA